HEADER OXYGEN STORAGE/TRANSPORT 09-JAN-02 1KR7 TITLE CRYSTAL STRUCTURE OF THE NERVE TISSUE MINI-HEMOGLOBIN FROM TITLE 2 THE NEMERTEAN WORM CEREBRATULUS LACTEUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEURAL GLOBIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MINI-HEMOGLOBIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CEREBRATULUS LACTEUS; SOURCE 3 ORGANISM_COMMON: MILKY RIBBON-WORM; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS NERVE TISSUE, MINI-HEMOGLOBIN, PROTEIN CAVITIES, OXYGEN KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.PESCE,M.NARDINI,S.DEWILDE,E.GEUENS,K.YAMAUCHI,P.ASCENZI, AUTHOR 2 A.F.RIGGS,L.MOENS,M.BOLOGNESI REVDAT 2 01-APR-03 1KR7 1 JRNL REVDAT 1 15-MAY-02 1KR7 0 JRNL AUTH A.PESCE,M.NARDINI,S.DEWILDE,E.GEUENS,K.YAMAUCHI, JRNL AUTH 2 P.ASCENZI,A.F.RIGGS,L.MOENS,M.BOLOGNESI JRNL TITL THE 109 RESIDUE NERVE TISSUE MINIHEMOGLOBIN FROM JRNL TITL 2 CEREBRATULUS LACTEUS HIGHLIGHTS STRIKING JRNL TITL 3 STRUCTURAL PLASTICITY OF THE ALPHA-HELICAL GLOBIN JRNL TITL 4 FOLD JRNL REF STRUCTURE V. 10 725 2002 JRNL REFN ASTM STRUE6 UK ISSN 0969-2126 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.PESCE,M.NARDINI,S.DEWILDE,P.ASCENZI,A.F.RIGGS, REMARK 1 AUTH 2 K.YAMAUCHI,E.GEUENS,L.MOENS,M.BOLOGNESI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF REMARK 1 TITL 2 NEURAL HEMOGLOBIN FROM THE NEMERTEAN WORM REMARK 1 TITL 3 CEREBRATULUS LACTEUS REMARK 1 REF ACTA CRYSTALLOGR., SECT.D V. 57 1897 2001 REMARK 1 REFN ASTM ABCRE6 DK ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 16071 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1808 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 814 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : -0.27000 REMARK 3 B33 (A**2) : -0.20000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.044 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.824 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.006 ; 0.021 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) : 1.188 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.093 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.246 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.333 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KR7 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 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB . REMARK 100 THE RCSB ID CODE IS RCSB015258. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-2001 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.739, 1.740, 0.915 REMARK 200 MONOCHROMATOR : SI 311 CHANNEL AND SI 111 REMARK 200 CHANNEL CUT REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17906 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.23900 REMARK 200 R SYM FOR SHELL (I) : 0.23900 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM ACETATE, REMARK 280 PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 21.36050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.05500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.58650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.05500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.36050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.58650 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 O4 SO4 152 O HOH 97 1.77 REMARK 500 O1A HEM A 144 O HOH 42 1.97 REMARK 500 O1 SO4 152 O HOH 97 2.13 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH 4 O HOH 247 3655 0.52 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 16 CE LYS A 16 NZ 0.271 REMARK 500 LYS A 36 CG LYS A 36 CD 0.135 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 16 CD - CE - NZ ANGL. DEV. =-18.7 DEGREES DBREF 1KR7 A 0 109 UNP O76242 GLBN_CERLA 1 110 SEQRES 1 A 110 MET VAL ASN TRP ALA ALA VAL VAL ASP ASP PHE TYR GLN SEQRES 2 A 110 GLU LEU PHE LYS ALA HIS PRO GLU TYR GLN ASN LYS PHE SEQRES 3 A 110 GLY PHE LYS GLY VAL ALA LEU GLY SER LEU LYS GLY ASN SEQRES 4 A 110 ALA ALA TYR LYS THR GLN ALA GLY LYS THR VAL ASP TYR SEQRES 5 A 110 ILE ASN ALA ALA ILE GLY GLY SER ALA ASP ALA ALA GLY SEQRES 6 A 110 LEU ALA SER ARG HIS LYS GLY ARG ASN VAL GLY SER ALA SEQRES 7 A 110 GLU PHE HIS ASN ALA LYS ALA CYS LEU ALA LYS ALA CYS SEQRES 8 A 110 SER ALA HIS GLY ALA PRO ASP LEU GLY HIS ALA ILE ASP SEQRES 9 A 110 ASP ILE LEU SER HIS LEU HET SO4 152 5 HET ACT 153 4 HET HEM A 144 43 HET OXY A 150 2 HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM OXY OXYGEN MOLECULE HETSYN HEM HEME FORMUL 2 SO4 O4 S 2- FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 5 OXY O2 FORMUL 6 HOH *106(H2 O) HELIX 1 1 ASN A 2 HIS A 18 1 17 HELIX 2 2 PRO A 19 PHE A 25 5 7 HELIX 3 3 ALA A 31 GLY A 37 5 7 HELIX 4 4 ASN A 38 GLY A 58 1 21 HELIX 5 5 ASP A 61 GLY A 71 1 11 HELIX 6 6 GLY A 75 HIS A 93 1 19 HELIX 7 7 LEU A 98 SER A 107 1 10 LINK FE HEM A 144 NE2 HIS A 69 LINK FE HEM A 144 O1 OXY A 150 CRYST1 42.721 43.173 60.110 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 0.023408 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023163 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016636 0.00000