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HEADER OXYGEN STORAGE 22-FEB-89 4MBA TITLE APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT TITLE 2 1.6 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: APLYSIA LIMACINA KEYWDS OXYGEN STORAGE EXPDTA X-RAY DIFFRACTION AUTHOR M.BOLOGNESI,S.ONESTI,G.GATTI,A.CODA,P.ASCENZI,M.BRUNORI REVDAT 3 01-APR-03 4MBA 1 JRNL REVDAT 2 15-APR-92 4MBA 3 ATOM REVDAT 1 15-JAN-90 4MBA 0 JRNL AUTH M.BOLOGNESI,S.ONESTI,G.GATTI,A.CODA,P.ASCENZI, JRNL AUTH 2 M.BRUNORI JRNL TITL APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC JRNL TITL 2 ANALYSIS AT 1.6 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 205 529 1989 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.BOLOGNESI,G.GATTI,M.G.GUANZIROLI,A.MATTEVI, REMARK 1 AUTH 2 S.ONESTI,A.CODA,P.ASCENZI,M.BRUNORI REMARK 1 TITL APLYSIA LIMACINA MYOGLOBIN. MOLECULAR BASES FOR REMARK 1 TITL 2 LIGAND BINDING AND REVERSIBLE UNFOLDING REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH M.BOLOGNESI,A.CODA,G.GATTI,P.ASCENZI,M.BRUNORI REMARK 1 TITL CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA REMARK 1 TITL 2 MYOGLOBIN AT 2.0 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 183 113 1985 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.BOLOGNESI,E.CANNILLO,P.ASCENZI,G.M.GIACOMETTI, REMARK 1 AUTH 2 A.MERLI,M.BRUNORI REMARK 1 TITL REACTIVITY OF FERRIC APLYSIA AND SPERM WHALE REMARK 1 TITL 2 MYOGLOBINS TOWARDS IMIDAZOLE. X-RAY AND BINDING REMARK 1 TITL 3 STUDY REMARK 1 REF J.MOL.BIOL. V. 158 305 1982 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.BOLOGNESI,E.CANNILLO,R.OBERTI,G.ROSSI,L.UNGARETTI REMARK 1 TITL THE STRUCTURE OF APLYSIA LIMACINA MYOGLOBIN AT 3.6 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.A V. 34 62 1978 REMARK 1 REF 2 (SUPPLEMENT) REMARK 1 REFN ASTM ACACBN DK ISSN 0567-7394 REMARK 1 REFERENCE 5 REMARK 1 AUTH L.UNGARETTI,M.BOLOGNESI,E.CANNILLO,R.OBERTI,G.ROSSI REMARK 1 TITL THE CRYSTAL STRUCTURE OF MET-MYOGLOBIN FROM REMARK 1 TITL 2 APLYSIA LIMACINA AT 5 ANGSTROMS RESOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.B V. 34 3658 1978 REMARK 1 REFN ASTM ACBCAR DK ISSN 0567-7408 REMARK 1 REFERENCE 6 REMARK 1 AUTH T.L.BLUNDELL,M.BRUNORI,B.CURTI,M.BOLOGNESI,A.CODA, REMARK 1 AUTH 2 M.FUMAGALLI,L.UNGARETTI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION REMARK 1 TITL 2 STUDIES ON MET-MYOGLOBIN FROM APLYSIA LIMACINA REMARK 1 REF J.MOL.BIOL. V. 97 665 1975 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 7 REMARK 1 AUTH L.TENTORI,G.VIVALDI,S.CARTA,M.MARINUCCI,A.MASSA, REMARK 1 AUTH 2 E.ANTONINI,M.BRUNORI REMARK 1 TITL THE AMINO ACID SEQUENCE OF MYOGLOBIN FROM THE REMARK 1 TITL 2 MOLLUSC APLYSIA LIMACINA REMARK 1 REF INT.J.PEPT.PROTEIN RES. V. 5 187 1973 REMARK 1 REFN ASTM IJPPC3 DK ISSN 0367-8377 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD :NULL REMARK 3 FREE R VALUE TEST SET SELECTION :NULL REMARK 3 R VALUE (WORKING + TEST SET) :0.180 REMARK 3 R VALUE (WORKING SET) :NULL 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 USING ALL DATA, NO SIGMA CUTOFF. 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 : 1086 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 107 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.013 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.310 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4MBA 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 (2007-03-18) 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 : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 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 26.45000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.25000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.45000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.20000 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 NE2 HIS A 95 FE HEM 148 2.13 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 170 DISTANCE = 5.38 ANGSTROMS REMARK 525 HOH 181 DISTANCE = 9.32 ANGSTROMS REMARK 525 HOH 184 DISTANCE = 5.29 ANGSTROMS REMARK 525 HOH 205 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH 209 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH 220 DISTANCE = 9.92 ANGSTROMS REMARK 525 HOH 222 DISTANCE = 5.66 ANGSTROMS REMARK 525 HOH 223 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH 225 DISTANCE = 5.42 ANGSTROMS REMARK 525 HOH 230 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH 231 DISTANCE = 8.61 ANGSTROMS REMARK 525 HOH 237 DISTANCE = 8.43 ANGSTROMS REMARK 525 HOH 250 DISTANCE = 5.10 ANGSTROMS REMARK 525 HOH 283 DISTANCE = 6.11 ANGSTROMS DBREF 4MBA A 1 145 UNP P02210 GLB_APLLI 1 145 SEQADV 4MBA ASN A 22 UNP P02210 ASP 22 CONFLICT SEQADV 4MBA LEU A 26 UNP P02210 ASP 26 CONFLICT SEQADV 4MBA ASP A 27 UNP P02210 ALA 27 CONFLICT SEQADV 4MBA ASN A 80 UNP P02210 ASP 80 CONFLICT SEQRES 1 A 146 SER LEU SER ALA ALA GLU ALA ASP LEU ALA GLY LYS SER SEQRES 2 A 146 TRP ALA PRO VAL PHE ALA ASN LYS ASN ALA ASN GLY LEU SEQRES 3 A 146 ASP PHE LEU VAL ALA LEU PHE GLU LYS PHE PRO ASP SER SEQRES 4 A 146 ALA ASN PHE PHE ALA ASP PHE LYS GLY LYS SER VAL ALA SEQRES 5 A 146 ASP ILE LYS ALA SER PRO LYS LEU ARG ASP VAL SER SER SEQRES 6 A 146 ARG ILE PHE THR ARG LEU ASN GLU PHE VAL ASN ASN ALA SEQRES 7 A 146 ALA ASN ALA GLY LYS MET SER ALA MET LEU SER GLN PHE SEQRES 8 A 146 ALA LYS GLU HIS VAL GLY PHE GLY VAL GLY SER ALA GLN SEQRES 9 A 146 PHE GLU ASN VAL ARG SER MET PHE PRO GLY PHE VAL ALA SEQRES 10 A 146 SER VAL ALA ALA PRO PRO ALA GLY ALA ASP ALA ALA TRP SEQRES 11 A 146 THR LYS LEU PHE GLY LEU ILE ILE ASP ALA LEU LYS ALA SEQRES 12 A 146 ALA GLY ALA HET ACE A 0 3 HET HEM 148 43 HET IMD 149 5 HETNAM ACE ACETYL GROUP HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM IMD IMIDAZOLE HETSYN HEM HEME FORMUL 2 ACE C2 H4 O FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 IMD C3 H5 N2 1+ FORMUL 5 HOH *107(H2 O) HELIX 1 A ALA A 4 ALA A 19 1BENT ALPHA-HELIX, RESIDUE 16 16 HELIX 2 B LYS A 21 LYS A 35 1 15 HELIX 3 C PRO A 37 PHE A 42 5 6 HELIX 4 D VAL A 51 LYS A 55 1 5 HELIX 5 E LYS A 59 ASN A 76 1 18 HELIX 6 F ALA A 81 GLY A 97 1 17 HELIX 7 G SER A 102 SER A 118 1BENT ALPHA-HELIX, RESIDUE 113 17 HELIX 8 H ALA A 126 ALA A 143 1 18 LINK C ACE A 0 N SER A 1 CRYST1 52.900 70.400 32.500 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 0.018904 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014205 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030769 0.00000