HEADER OXYGEN BINDING, TRANSPORT PROTEIN 08-JAN-08 2ZFO TITLE STRUCTURE OF THE PARTIALLY UNLIGANDED MET STATE OF 400 KDA HEMOGLOBIN: TITLE 2 INSIGHTS INTO LIGAND-INDUCED STRUCTURAL CHANGES OF GIANT HEMOGLOBINS CAVEAT 2ZFO CHIRALITY ERRORS AT THE CB(B) CENTER OF ILE B 31 AND 69 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXTRACELLULAR GIANT HEMOGLOBIN MAJOR GLOBIN SUBUNIT A1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MAJOR GLOBIN CHAIN B; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: EXTRACELLULAR GIANT HEMOGLOBIN MAJOR GLOBIN SUBUNIT A2; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: MAJOR GLOBIN CHAIN A5; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: EXTRACELLULAR GIANT HEMOGLOBIN MAJOR GLOBIN SUBUNIT B2; COMPND 11 CHAIN: C; COMPND 12 SYNONYM: MAJOR GLOBIN CHAIN C; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: EXTRACELLULAR GIANT HEMOGLOBIN MAJOR GLOBIN SUBUNIT B1; COMPND 15 CHAIN: D; COMPND 16 SYNONYM: MAJOR GLOBIN CHAIN D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OLIGOBRACHIA MASHIKOI; SOURCE 3 ORGANISM_COMMON: BEARD WORM; SOURCE 4 ORGANISM_TAXID: 55676; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: OLIGOBRACHIA MASHIKOI; SOURCE 7 ORGANISM_COMMON: BEARD WORM; SOURCE 8 ORGANISM_TAXID: 55676; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: OLIGOBRACHIA MASHIKOI; SOURCE 11 ORGANISM_COMMON: BEARD WORM; SOURCE 12 ORGANISM_TAXID: 55676; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: OLIGOBRACHIA MASHIKOI; SOURCE 15 ORGANISM_COMMON: BEARD WORM; SOURCE 16 ORGANISM_TAXID: 55676 KEYWDS HEMOGLOBIN, POLYCHAETE, ANNELIDA, UNLIGANDED, HEME, IRON, METAL- KEYWDS 2 BINDING, OXYGEN TRANSPORT, SECRETED, TRANSPORT, OXYGEN BINDING, KEYWDS 3 TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.NUMOTO,T.NAKAGAWA,A.KITA,Y.SASAYAMA,Y.FUKUMORI,K.MIKI REVDAT 5 13-JUL-11 2ZFO 1 VERSN REVDAT 4 08-SEP-09 2ZFO 1 CAVEAT REVDAT 3 24-FEB-09 2ZFO 1 VERSN REVDAT 2 26-AUG-08 2ZFO 1 JRNL ATOM REVDAT 1 22-APR-08 2ZFO 0 JRNL AUTH N.NUMOTO,T.NAKAGAWA,A.KITA,Y.SASAYAMA,Y.FUKUMORI,K.MIKI JRNL TITL STRUCTURE OF THE PARTIALLY UNLIGANDED MET STATE OF 400 KDA JRNL TITL 2 HEMOGLOBIN: INSIGHTS INTO LIGAND-INDUCED STRUCTURAL CHANGES JRNL TITL 3 OF GIANT HEMOGLOBINS JRNL REF PROTEINS V. 73 113 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18398907 JRNL DOI 10.1002/PROT.22040 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 4031385.320 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 46892 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 SET) : 0.169 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2332 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4340 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 230 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4339 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 186 REMARK 3 SOLVENT ATOMS : 523 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.57000 REMARK 3 B22 (A**2) : 4.57000 REMARK 3 B33 (A**2) : -9.14000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.14 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.95 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.260 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.840 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.030 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.840 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 70.21 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : HEM_O2_FINAL.PARAM REMARK 3 PARAMETER FILE 4 : GOL_FINAL.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : HEM_O2_FINAL.TOP REMARK 3 TOPOLOGY FILE 4 : GOL_FINAL.PAR REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2ZFO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JAN-08. REMARK 100 THE RCSB ID CODE IS RCSB027912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : FIXED EXIT SI 111 DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : RH-COATED CYLINDRICAL BENDING REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47042 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 32.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33700 REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2D2M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7% PEG 10000, 0.2M TRIS-HCL (PH 8.0), REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 55.48000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 32.03139 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 90.52667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 55.48000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 32.03139 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 90.52667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 55.48000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 32.03139 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 90.52667 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 55.48000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 32.03139 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 90.52667 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 55.48000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 32.03139 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 90.52667 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 55.48000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 32.03139 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 90.52667 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 64.06279 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 181.05333 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 64.06279 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 181.05333 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 64.06279 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 181.05333 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 64.06279 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 181.05333 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 64.06279 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 181.05333 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 64.06279 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 181.05333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: 24-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 24-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 91850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 110740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -731.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C1277 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1269 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 2 77.78 68.51 REMARK 500 ALA A 21 -135.25 49.20 REMARK 500 ASP C 26 -6.10 65.95 REMARK 500 ASP C 83 69.09 -155.58 REMARK 500 CYS D 3 73.71 61.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 CYS B 2 10.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH C1287 DISTANCE = 5.42 ANGSTROMS REMARK 525 HOH C1431 DISTANCE = 5.57 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HEM A 200 NA 88.5 REMARK 620 3 HEM A 200 NB 87.6 89.6 REMARK 620 4 HEM A 200 NC 98.4 172.9 89.1 REMARK 620 5 HEM A 200 ND 97.9 89.7 174.5 90.9 REMARK 620 6 OXY A 201 O1 178.3 93.2 92.7 79.9 81.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 94 NE2 REMARK 620 2 HEM B 200 NA 88.4 REMARK 620 3 HEM B 200 NB 88.4 89.2 REMARK 620 4 HEM B 200 NC 100.1 171.4 89.6 REMARK 620 5 HEM B 200 ND 100.9 89.5 170.5 90.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM C 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 98 NE2 REMARK 620 2 HEM C 200 NA 95.2 REMARK 620 3 HEM C 200 NB 88.0 89.3 REMARK 620 4 HEM C 200 NC 90.6 174.1 90.2 REMARK 620 5 HEM C 200 ND 98.7 89.5 173.3 90.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM D 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 96 NE2 REMARK 620 2 HEM D 200 NA 93.6 REMARK 620 3 HEM D 200 NB 90.2 89.8 REMARK 620 4 HEM D 200 NC 93.1 173.3 89.5 REMARK 620 5 HEM D 200 ND 100.5 89.7 169.4 89.7 REMARK 620 N 1 2 3 4 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM C 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM D 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D2M RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN THE OXY FORM REMARK 900 RELATED ID: 2D2N RELATED DB: PDB REMARK 900 THE SAME PROTEIN, HG DERIVATIVE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CHAIN D (SUBUNIT B1) IS THE MIXTURE OF TWO ISOFORMS REMARK 999 (B1A AND B1B) CONTAINING 10 SUBSTITUTED RESIDUES IN EACH REMARK 999 145 AMINO ACIDS. REMARK 999 WE CONSTRUCTED THE MODEL BASICALLY BY USING THE SEQUENCE REMARK 999 OF B1A AND INCLUDED THE MODELS OF THE 10 SUBSTITUTED REMARK 999 RESIDUES OF THE B1B AS PSEUDO DOUBLE CONFORMATIONS, BECAUSE REMARK 999 INCLUDING OF THE FULL LENGTH OF BOTH B1A AND B1B WITH A REMARK 999 50/50 DISTRIBUTION WILL RESULTS IN UNDESIRED INCREASES REMARK 999 IN THE PARAMETERS. DBREF 2ZFO A 1 140 UNP Q7M419 GLBA1_OLIMA 17 156 DBREF 2ZFO B 1 142 UNP Q7M413 GLBA2_OLIMA 17 158 DBREF 2ZFO C 1 147 UNP Q7M418 GLBB2_OLIMA 17 163 DBREF 2ZFO D 1 145 UNP Q5KSB7 GLBB1_OLIMA 17 161 SEQADV 2ZFO ILE D 31 UNP Q5KSB7 VAL 47 MICROHETEROGENEITY SEQADV 2ZFO VAL D 38 UNP Q5KSB7 ALA 54 MICROHETEROGENEITY SEQADV 2ZFO THR D 41 UNP Q5KSB7 ALA 57 MICROHETEROGENEITY SEQADV 2ZFO SER D 57 UNP Q5KSB7 ASN 73 MICROHETEROGENEITY SEQADV 2ZFO SER D 58 UNP Q5KSB7 ASN 74 MICROHETEROGENEITY SEQADV 2ZFO ALA D 59 UNP Q5KSB7 PRO 75 MICROHETEROGENEITY SEQADV 2ZFO ILE D 69 UNP Q5KSB7 VAL 85 MICROHETEROGENEITY SEQADV 2ZFO LYS D 97 UNP Q5KSB7 ARG 113 MICROHETEROGENEITY SEQADV 2ZFO GLU D 112 UNP Q5KSB7 GLN 128 MICROHETEROGENEITY SEQADV 2ZFO GLY D 131 UNP Q5KSB7 GLU 147 MICROHETEROGENEITY SEQRES 1 A 140 VAL CYS ASN ARG LEU GLU GLN ILE LEU VAL LYS THR GLN SEQRES 2 A 140 TRP ALA GLN SER TYR GLY GLU ALA GLU ASN ARG ALA ALA SEQRES 3 A 140 PHE SER ARG ASP LEU PHE SER GLU LEU PHE ASN ILE GLN SEQRES 4 A 140 GLY SER SER ARG ALA LEU PHE SER GLY VAL GLY VAL ASP SEQRES 5 A 140 ASP MET ASN SER ALA ALA PHE THR ALA HIS CYS LEU ARG SEQRES 6 A 140 VAL THR GLY ALA LEU ASN ARG LEU ILE SER GLN LEU ASP SEQRES 7 A 140 GLN GLN ALA THR ILE ASN ALA ASP LEU ALA HIS LEU ALA SEQRES 8 A 140 GLY GLN HIS ALA SER ARG ASN LEU ASP ALA SER ASN PHE SEQRES 9 A 140 ALA ALA MET GLY GLN ALA VAL MET SER VAL VAL PRO THR SEQRES 10 A 140 HIS LEU ASP CYS PHE ASN GLN HIS ALA TRP GLY GLU CYS SEQRES 11 A 140 TYR GLU ARG ILE ALA SER GLY ILE SER GLY SEQRES 1 B 142 ASP CYS THR SER LEU ASN ARG LEU LEU VAL LYS ARG GLN SEQRES 2 B 142 TRP ALA GLU ALA TYR GLY GLU GLY THR ASN ARG GLU LEU SEQRES 3 B 142 LEU GLY ASN ARG ILE TRP GLU ASP LEU PHE ALA ASN MET SEQRES 4 B 142 PRO ASP ALA ARG GLY LEU PHE SER ARG VAL ASN GLY ASN SEQRES 5 B 142 ASP ILE ASP SER SER GLU PHE GLN ALA HIS SER LEU ARG SEQRES 6 B 142 VAL LEU GLY GLY LEU ASP MET CYS VAL ALA SER LEU ASP SEQRES 7 B 142 ASP VAL PRO VAL LEU ASN ALA LEU LEU ALA ARG LEU ASN SEQRES 8 B 142 SER GLN HIS ASP SER ARG GLY ILE PRO ALA ALA GLY TYR SEQRES 9 B 142 PRO ALA PHE VAL ALA SER ALA ILE SER ALA VAL ARG ALA SEQRES 10 B 142 THR VAL GLY ALA ARG SER PHE ASP ASN ASP ALA TRP ASN SEQRES 11 B 142 SER CYS MET ASN GLN ILE VAL SER GLY ILE SER GLY SEQRES 1 C 147 SER SER CYS CYS SER SER GLU ASP ARG ALA ASN VAL MET SEQRES 2 C 147 HIS ASN TRP ASP ALA ALA TRP SER ALA ALA TYR SER ASP SEQRES 3 C 147 ARG ARG VAL ALA LEU ALA GLN ALA VAL PHE ALA SER LEU SEQRES 4 C 147 PHE SER ARG ASP ALA ALA ALA GLN GLY LEU PHE SER GLY SEQRES 5 C 147 VAL SER ALA ASP ASN PRO ASP SER ALA ASP PHE ARG ALA SEQRES 6 C 147 HIS CYS VAL ARG VAL VAL ASN GLY LEU ASP VAL ALA ILE SEQRES 7 C 147 ASN MET LEU ASN ASP PRO ALA VAL LEU ASN GLU GLN LEU SEQRES 8 C 147 ALA HIS LEU SER ALA GLN HIS GLN ALA ARG ALA GLY VAL SEQRES 9 C 147 ALA ALA ALA HIS PHE ASP VAL MET ALA GLU ALA PHE ALA SEQRES 10 C 147 GLU VAL MET PRO GLN VAL SER SER CYS PHE SER SER ASP SEQRES 11 C 147 SER TRP ASN ARG CYS PHE ALA ARG ILE ALA ASN GLY ILE SEQRES 12 C 147 SER ALA GLY LEU SEQRES 1 D 145 GLU CYS CYS SER ARG GLY ASP ALA GLU VAL VAL ILE SER SEQRES 2 D 145 GLU TRP ASP GLN VAL PHE ASN ALA ALA MET ALA GLY SER SEQRES 3 D 145 SER GLU SER ALA ILE GLY VAL ALA ILE PHE ASP VAL PHE SEQRES 4 D 145 PHE THR SER SER GLY VAL SER PRO SER MET PHE PRO GLY SEQRES 5 D 145 GLY GLY ASP SER SER SER ALA GLU PHE LEU ALA GLN VAL SEQRES 6 D 145 SER ARG VAL ILE SER GLY ALA ASP ILE ALA ILE ASN SER SEQRES 7 D 145 LEU THR ASN ARG ALA THR CYS ASP SER LEU LEU SER HIS SEQRES 8 D 145 LEU ASN ALA GLN HIS LYS ALA ILE SER GLY VAL THR GLY SEQRES 9 D 145 ALA ALA VAL THR HIS LEU SER GLU ALA ILE SER SER VAL SEQRES 10 D 145 VAL ALA GLN VAL LEU PRO SER ALA HIS ILE ASP ALA TRP SEQRES 11 D 145 GLY TYR CYS MET ALA TYR ILE ALA ALA GLY ILE GLY ALA SEQRES 12 D 145 GLY LEU HET HEM A 200 43 HET OXY A 201 2 HET HEM B 200 43 HET GOL B 501 6 HET HEM C 200 43 HET GOL C 502 6 HET HEM D 200 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM OXY OXYGEN MOLECULE HETNAM GOL GLYCEROL HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 HEM 4(C34 H32 FE N4 O4) FORMUL 6 OXY O2 FORMUL 8 GOL 2(C3 H8 O3) FORMUL 12 HOH *523(H2 O) HELIX 1 1 ASN A 3 TYR A 18 1 16 HELIX 2 2 GLU A 22 ILE A 38 1 17 HELIX 3 3 GLN A 39 SER A 47 5 9 HELIX 4 4 SER A 56 SER A 75 1 20 HELIX 5 5 GLN A 79 HIS A 94 1 16 HELIX 6 6 ASP A 100 VAL A 115 1 16 HELIX 7 7 PRO A 116 LEU A 119 5 4 HELIX 8 8 ASN A 123 ILE A 138 1 16 HELIX 9 9 THR B 3 TYR B 18 1 16 HELIX 10 10 THR B 22 ASN B 38 1 17 HELIX 11 11 MET B 39 SER B 47 5 9 HELIX 12 12 SER B 56 LEU B 77 1 22 HELIX 13 13 ASP B 79 HIS B 94 1 16 HELIX 14 14 ALA B 102 VAL B 119 1 18 HELIX 15 15 ASP B 125 SER B 141 1 17 HELIX 16 16 SER C 5 TRP C 20 1 16 HELIX 17 17 ASP C 26 ARG C 42 1 17 HELIX 18 18 ASP C 43 SER C 51 5 9 HELIX 19 19 SER C 60 ASN C 79 1 20 HELIX 20 20 ASP C 83 ALA C 100 1 18 HELIX 21 21 ALA C 107 VAL C 123 1 17 HELIX 22 22 SER C 128 SER C 144 1 17 HELIX 23 23 SER D 4 VAL D 18 1 15 HELIX 24 24 GLY D 25 GLY D 44 1 20 HELIX 25 25 SER D 58 ASN D 77 1 20 HELIX 26 26 ASN D 81 ALA D 98 1 18 HELIX 27 27 THR D 103 VAL D 121 1 19 HELIX 28 28 HIS D 126 GLY D 142 1 17 SSBOND 1 CYS A 2 CYS A 130 1555 1555 2.03 SSBOND 2 CYS A 121 CYS C 126 1555 1555 2.04 SSBOND 3 CYS B 2 CYS B 132 1555 1555 2.03 SSBOND 4 CYS C 3 CYS D 2 1555 2555 2.34 SSBOND 5 CYS C 4 CYS C 135 1555 1555 2.04 SSBOND 6 CYS D 3 CYS D 133 1555 1555 2.06 LINK NE2 HIS A 94 FE HEM A 200 1555 1555 2.13 LINK NE2 HIS B 94 FE HEM B 200 1555 1555 2.20 LINK NE2 HIS C 98 FE HEM C 200 1555 1555 2.31 LINK NE2 HIS D 96 FE HEM D 200 1555 1555 2.16 LINK FE HEM A 200 O1 OXY A 201 1555 1555 1.83 SITE 1 AC1 17 LEU A 45 PHE A 46 VAL A 49 ARG A 65 SITE 2 AC1 17 HIS A 94 ARG A 97 LEU A 99 ASN A 103 SITE 3 AC1 17 TYR A 131 ILE A 138 OXY A 201 HOH A1102 SITE 4 AC1 17 HOH A1188 HOH A1193 HIS D 91 GLN D 95 SITE 5 AC1 17 HOH D1197 SITE 1 AC2 5 PHE A 32 PHE A 46 HIS A 62 VAL A 66 SITE 2 AC2 5 HEM A 200 SITE 1 AC3 18 LEU B 45 PHE B 46 ARG B 48 VAL B 49 SITE 2 AC3 18 ARG B 65 GLY B 69 LEU B 70 GLN B 93 SITE 3 AC3 18 HIS B 94 ILE B 99 GLY B 103 TYR B 104 SITE 4 AC3 18 PHE B 107 ILE B 140 HOH B1027 HOH B1339 SITE 5 AC3 18 HIS C 93 GLN C 97 SITE 1 AC4 6 GLU B 20 GLY B 21 THR B 22 ASN B 23 SITE 2 AC4 6 HOH B1227 ASN C 82 SITE 1 AC5 19 ARG B 89 GLN B 93 LEU C 49 PHE C 50 SITE 2 AC5 19 VAL C 53 HIS C 66 ARG C 69 VAL C 70 SITE 3 AC5 19 GLY C 73 LEU C 74 GLN C 97 HIS C 98 SITE 4 AC5 19 ARG C 101 HIS C 108 PHE C 109 MET C 112 SITE 5 AC5 19 ILE C 143 HOH C1125 HOH C1463 SITE 1 AC6 10 ARG B 122 ASN C 82 ASP C 83 PRO C 84 SITE 2 AC6 10 HOH C1057 HOH C1439 SER D 124 ALA D 125 SITE 3 AC6 10 HIS D 126 HOH D1281 SITE 1 AC7 18 HIS A 89 GLN A 93 HOH A1049 HOH A1193 SITE 2 AC7 18 MET D 49 PHE D 50 GLN D 64 ARG D 67 SITE 3 AC7 18 VAL D 68 ALA D 72 HIS D 96 ILE D 99 SITE 4 AC7 18 ALA D 106 VAL D 107 LEU D 110 ILE D 141 SITE 5 AC7 18 HOH D1009 HOH D1237 CRYST1 110.960 110.960 271.580 90.00 90.00 120.00 H 3 2 18 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 0.009012 0.005203 0.000000 0.00000 SCALE2 0.000000 0.010406 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003682 0.00000 MASTER 447 0 7 28 0 0 27 6 0 0 0 46 END