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HEADER OXYGEN TRANSPORT 22-FEB-95 1EMY TITLE CRYSTAL STRUCTURE OF ASIAN ELEPHANT (ELEPHAS MAXIMUS) CYANO- TITLE 2 MET MYOGLOBIN AT 1.78 ANGSTROMS RESOLUTION. PHE 29 (B10) TITLE 3 ACCOUNTS FOR ITS UNUSUAL LIGAND BINDING PROPERTIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ELEPHAS MAXIMUS; SOURCE 3 ORGAN: SKELETAL KEYWDS HEME PROTEIN, GLOBIN FOLD EXPDTA X-RAY DIFFRACTION AUTHOR D.A.BISIG,K.PIONTEK REVDAT 2 03-MAY-05 1EMY 1 REMARK REVDAT 1 20-APR-95 1EMY 0 JRNL AUTH D.A.BISIG,E.E.DI IORIO,K.DIEDERICHS, JRNL AUTH 2 K.H.WINTERHALTER,K.PIONTEK JRNL TITL CRYSTAL STRUCTURE OF ASIAN ELEPHANT (ELEPHAS JRNL TITL 2 MAXIMUS) CYANO-METMYOGLOBIN AT 1.78-A RESOLUTION. JRNL TITL 3 PHE29(B10) ACCOUNTS FOR ITS UNUSUAL LIGAND BINDING JRNL TITL 4 PROPERTIES. JRNL REF J.BIOL.CHEM. V. 270 20754 1995 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.ZHAO,K.VYAS,B.D.NGUYEN,K.RAJARATHNAM,G.N.LA MAR, REMARK 1 AUTH 2 T.LI,G.N.PHILLIPS JR.,R.F.EICH,J.S.OLSON,J.LING, REMARK 1 AUTH 3 D.F.BOCIAN REMARK 1 TITL A DOUBLE MUTANT OF SPERM WHALE MYOGLOBIN MIMICS REMARK 1 TITL 2 THE STRUCTURE AND FUNCTION OF ELEPHANT MYOGLOBIN REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH K.VYAS,K.RAJARATHNAM,L.P.YU,S.D.EMERSON,G.N.LA MAR, REMARK 1 AUTH 2 R.KRISHNAMOORTHI REMARK 1 TITL 1H NMR INVESTIGATION OF THE HEME CAVITY OF REMARK 1 TITL 2 ELEPHANT (E7 GLN) MET-CYANO-MYOGLOBIN. EVIDENCE REMARK 1 TITL 3 FOR A B-HELIX PHENYLALANINE INTERACTION WITH BOUND REMARK 1 TITL 4 LIGAND REMARK 1 REF J.BIOL.CHEM. V. 268 14826 1993 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ, X-PLOR REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12966 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1202 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 219 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.10 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.801 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.579 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.502 ; 1.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.518 ; 1.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EMY COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-17) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13649 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 16.75500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.22000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.22000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.75500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.29500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 C CYN 155 FE HEM 154 1.85 REMARK 500 O HOH 281 O HOH 313 1.86 REMARK 500 O HOH 311 O HOH 389 2.06 REMARK 500 O HOH 242 O HOH 341 2.07 REMARK 500 NE2 HIS A 93 FE HEM 154 2.11 REMARK 500 O HOH 290 O HOH 375 2.16 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 200 DISTANCE = 7.56 ANGSTROMS REMARK 525 HOH 208 DISTANCE = 7.46 ANGSTROMS REMARK 525 HOH 211 DISTANCE = 13.19 ANGSTROMS REMARK 525 HOH 213 DISTANCE = 9.28 ANGSTROMS REMARK 525 HOH 215 DISTANCE = 8.25 ANGSTROMS REMARK 525 HOH 221 DISTANCE = 12.80 ANGSTROMS REMARK 525 HOH 237 DISTANCE = 5.19 ANGSTROMS REMARK 525 HOH 246 DISTANCE = 10.78 ANGSTROMS REMARK 525 HOH 250 DISTANCE = 8.49 ANGSTROMS REMARK 525 HOH 251 DISTANCE = 8.84 ANGSTROMS REMARK 525 HOH 263 DISTANCE = 9.56 ANGSTROMS REMARK 525 HOH 270 DISTANCE = 5.71 ANGSTROMS REMARK 525 HOH 273 DISTANCE = 5.21 ANGSTROMS REMARK 525 HOH 320 DISTANCE = 18.68 ANGSTROMS REMARK 525 HOH 339 DISTANCE = 9.24 ANGSTROMS REMARK 525 HOH 342 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH 343 DISTANCE = 9.54 ANGSTROMS REMARK 525 HOH 353 DISTANCE = 9.75 ANGSTROMS REMARK 525 HOH 356 DISTANCE = 10.03 ANGSTROMS REMARK 525 HOH 357 DISTANCE = 7.19 ANGSTROMS REMARK 525 HOH 358 DISTANCE = 11.94 ANGSTROMS REMARK 525 HOH 361 DISTANCE = 5.76 ANGSTROMS REMARK 525 HOH 366 DISTANCE = 8.55 ANGSTROMS REMARK 525 HOH 369 DISTANCE = 7.53 ANGSTROMS REMARK 525 HOH 372 DISTANCE = 9.18 ANGSTROMS REMARK 525 HOH 373 DISTANCE = 8.11 ANGSTROMS REMARK 525 HOH 383 DISTANCE = 5.45 ANGSTROMS REMARK 525 HOH 385 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH 386 DISTANCE = 10.07 ANGSTROMS REMARK 525 HOH 389 DISTANCE = 5.44 ANGSTROMS REMARK 525 HOH 395 DISTANCE = 8.73 ANGSTROMS REMARK 525 HOH 410 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH 416 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH 418 DISTANCE = 10.71 ANGSTROMS REMARK 525 HOH 435 DISTANCE = 5.39 ANGSTROMS REMARK 525 HOH 447 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH 454 DISTANCE = 9.30 ANGSTROMS DBREF 1EMY A 1 153 UNP P02186 MYG_ELEMA 1 153 SEQRES 1 A 153 GLY LEU SER ASP GLY GLU TRP GLU LEU VAL LEU LYS THR SEQRES 2 A 153 TRP GLY LYS VAL GLU ALA ASP ILE PRO GLY HIS GLY GLU SEQRES 3 A 153 THR VAL PHE VAL ARG LEU PHE THR GLY HIS PRO GLU THR SEQRES 4 A 153 LEU GLU LYS PHE ASP LYS PHE LYS HIS LEU LYS THR GLU SEQRES 5 A 153 GLY GLU MET LYS ALA SER GLU ASP LEU LYS LYS GLN GLY SEQRES 6 A 153 VAL THR VAL LEU THR ALA LEU GLY GLY ILE LEU LYS LYS SEQRES 7 A 153 LYS GLY HIS HIS GLU ALA GLU ILE GLN PRO LEU ALA GLN SEQRES 8 A 153 SER HIS ALA THR LYS HIS LYS ILE PRO ILE LYS TYR LEU SEQRES 9 A 153 GLU PHE ILE SER ASP ALA ILE ILE HIS VAL LEU GLN SER SEQRES 10 A 153 LYS HIS PRO ALA GLU PHE GLY ALA ASP ALA GLN GLY ALA SEQRES 11 A 153 MET LYS LYS ALA LEU GLU LEU PHE ARG ASN ASP ILE ALA SEQRES 12 A 153 ALA LYS TYR LYS GLU LEU GLY PHE GLN GLY HET CYN 155 2 HET HEM 154 43 HETNAM CYN CYANIDE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 CYN C N 1- FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 HOH *219(H2 O) HELIX 1 A ASP A 4 GLU A 18 1 15 HELIX 2 B ILE A 21 GLY A 35 1 15 HELIX 3 C PRO A 37 LYS A 42 5 6 HELIX 4 D GLU A 52 LYS A 56 1 5 HELIX 5 E GLU A 59 LYS A 77 1 19 HELIX 6 F GLU A 83 THR A 95 1 13 HELIX 7 G ILE A 101 LYS A 118 1 18 HELIX 8 H ALA A 125 GLU A 148 1 24 SITE 1 S1 3 GLN A 64 HIS A 93 PHE A 29 CRYST1 33.510 58.590 70.440 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.029842 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017068 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014196 0.00000