HEADER OXYGEN STORAGE 22-FEB-89 2MBA OBSLTE 15-JUL-92 2MBA 5MBA TITLE APLYSIA $LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT TITLE 2 1.6 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS OXYGEN STORAGE EXPDTA X-RAY DIFFRACTION AUTHOR M.BOLOGNESI,S.ONESTI,G.GATTI,A.CODA,P.ASCENZI,M.BRUNORI REVDAT 3 15-JUL-92 2MBA 3 OBSLTE REVDAT 2 15-APR-92 2MBA 3 ATOM REVDAT 1 15-JAN-90 2MBA 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 ANGSTROMS 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. NULL ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : NULL REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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 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 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 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 : 46 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MBA COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 2MBA AZIDE ION IS BOUND TO THE HEME IRON AT THE DISTAL REMARK 5 SITE. 2MBA REMARK 6 REMARK 6 2MBA CORRECTION. STANDARDIZE ATOM NAMING AND ORDERING FOR REMARK 6 ACE 2MBA RESIDUE. 15-APR-92. 2MBA REMARK 7 REMARK 7 2MBA CORRECTION. THIS ENTRY IS OBSOLETE. 15-JUL-92. 2MBA 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 (%): 37.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 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 26.49000 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 35.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 16.25000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.49000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.35000 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 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 95 FE HEM 148 2.15 REMARK 500 N3 AZI 149 FE HEM 148 2.15 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 181 DISTANCE = 9.31 ANGSTROMS REMARK 525 HOH 184 DISTANCE = 5.33 ANGSTROMS REMARK 525 HOH 193 DISTANCE = 5.37 ANGSTROMS REMARK 525 HOH 205 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH 209 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH 220 DISTANCE = 9.99 ANGSTROMS REMARK 525 HOH 222 DISTANCE = 5.24 ANGSTROMS REMARK 525 HOH 223 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH 225 DISTANCE = 5.31 ANGSTROMS REMARK 525 HOH 230 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH 231 DISTANCE = 9.25 ANGSTROMS REMARK 525 HOH 237 DISTANCE = 8.24 ANGSTROMS REMARK 525 HOH 240 DISTANCE = 5.55 ANGSTROMS REMARK 525 HOH 250 DISTANCE = 5.79 ANGSTROMS REMARK 525 HOH 276 DISTANCE = 8.41 ANGSTROMS REMARK 525 HOH 283 DISTANCE = 5.41 ANGSTROMS SEQRES 1 147 ACE SER LEU SER ALA ALA GLU ALA ASP LEU ALA GLY LYS SEQRES 2 147 SER TRP ALA PRO VAL PHE ALA ASN LYS ASN ALA ASN GLY SEQRES 3 147 LEU ASP PHE LEU VAL ALA LEU PHE GLU LYS PHE PRO ASP SEQRES 4 147 SER ALA ASN PHE PHE ALA ASP PHE LYS GLY LYS SER VAL SEQRES 5 147 ALA ASP ILE LYS ALA SER PRO LYS LEU ARG ASP VAL SER SEQRES 6 147 SER ARG ILE PHE THR ARG LEU ASN GLU PHE VAL ASN ASN SEQRES 7 147 ALA ALA ASN ALA GLY LYS MET SER ALA MET LEU SER GLN SEQRES 8 147 PHE ALA LYS GLU HIS VAL GLY PHE GLY VAL GLY SER ALA SEQRES 9 147 GLN PHE GLU ASN VAL ARG SER MET PHE PRO GLY PHE VAL SEQRES 10 147 ALA SER VAL ALA ALA PRO PRO ALA GLY ALA ASP ALA ALA SEQRES 11 147 TRP THR LYS LEU PHE GLY LEU ILE ILE ASP ALA LEU LYS SEQRES 12 147 ALA ALA GLY ALA HET ACE 0 3 HET AZI 149 3 HET HEM 148 43 HETNAM ACE ACETYL GROUP HETNAM AZI AZIDE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 1 ACE C2 H4 O FORMUL 2 AZI N3 1- FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 HOH *106(H2 O1) HELIX 1 A ALA 4 ALA 19 1BENT ALPHA-HELIX, RESIDUE 16 16 HELIX 2 B LYS 21 LYS 35 1 15 HELIX 3 C PRO 37 PHE 42 5 6 HELIX 4 D VAL 51 LYS 55 1 5 HELIX 5 E LYS 59 ASN 76 1 18 HELIX 6 F ALA 81 GLY 97 1 17 HELIX 7 G SER 102 SER 118 1BENT ALPHA-HELIX, RESIDUE 113 17 HELIX 8 H ALA 126 ALA 143 1 18 CRYST1 52.980 70.700 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 0.018875 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014144 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030769 0.00000 HETATM 1 C ACE 0 -71.088 -51.021 -24.644 1.00 28.19 C HETATM 2 O ACE 0 -70.801 -49.813 -24.485 1.00 26.13 O HETATM 3 CH3 ACE 0 -72.076 -51.504 -25.707 1.00 27.51 C