PDB Short entry for 3GVY HEADER METAL BINDING PROTEIN 31-MAR-09 3GVY TITLE CRYSTAL STRUCTURE OF BACTERIOFERRITIN FROM R.SPHAEROIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIOFERRITIN; COMPND 3 CHAIN: A, B, C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER SPHAEROIDES; SOURCE 3 ORGANISM_TAXID: 272943; SOURCE 4 STRAIN: 2.4.1; SOURCE 5 OTHER_DETAILS: NATIVE PROTEIN AS-ISOLATED KEYWDS BACTERIOFERRITIN, FERRITIN, IRON STORAGE, DI-IRON, FERROXIDASE KEYWDS 2 ACTIVITY, HEME, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.Y.HWANG,K.H.NAM REVDAT 5 01-NOV-23 3GVY 1 REMARK LINK REVDAT 4 01-NOV-17 3GVY 1 REMARK REVDAT 3 05-MAY-10 3GVY 1 SCALE3 REVDAT 2 02-FEB-10 3GVY 1 JRNL CRYST1 REVDAT 1 22-DEC-09 3GVY 0 JRNL AUTH K.H.NAM,Y.XU,S.PIAO,A.PRIYADARSHI,E.H.LEE,H.-Y.KIM,Y.H.JEON, JRNL AUTH 2 N.-C.HA,K.Y.HWANG JRNL TITL CRYSTAL STRUCTURE OF BACTERIOFERRITIN FROM RHODOBACTER JRNL TITL 2 SPHAEROIDES JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 391 990 2010 JRNL REFN ISSN 0006-291X JRNL PMID 19968959 JRNL DOI 10.1016/J.BBRC.2009.12.003 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 16139 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 866 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1053 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3832 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 89 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.05000 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): 1.968 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.414 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.276 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.789 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.877 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.782 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4007 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5433 ; 1.720 ; 2.022 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 470 ; 5.498 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 212 ;45.296 ;24.340 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 707 ;19.740 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;17.742 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 560 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3089 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2344 ; 0.659 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3739 ; 1.371 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1663 ; 2.279 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1694 ; 3.842 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 3GVY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000052374. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17331 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.14200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.35700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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 1JGC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA-CITRATE, PH5.6, 14-20% (W/V) REMARK 280 PEG 200, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 80.24750 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 80.24750 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 58.13800 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 80.24750 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 80.24750 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 58.13800 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 80.24750 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 80.24750 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 58.13800 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 80.24750 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 80.24750 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 58.13800 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 80.24750 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 80.24750 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 58.13800 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 80.24750 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 80.24750 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 58.13800 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 80.24750 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 80.24750 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 58.13800 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 80.24750 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 80.24750 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 58.13800 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: 97980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 126740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -971.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 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 116.27600 REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 116.27600 REMARK 350 BIOMT1 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 116.27600 REMARK 350 BIOMT1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 116.27600 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 FE HEM B 162 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 158 REMARK 465 GLU A 159 REMARK 465 ALA A 160 REMARK 465 GLU A 161 REMARK 465 GLU B 159 REMARK 465 ALA B 160 REMARK 465 GLU B 161 REMARK 465 GLU C 159 REMARK 465 ALA C 160 REMARK 465 GLU C 161 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 DISTANCE REMARK 500 NH1 ARG A 112 OD1 ASP B 106 2.05 REMARK 500 NE2 GLN A 137 OH TYR A 149 2.16 REMARK 500 SD MET B 52 NB HEM B 162 2.16 REMARK 500 SD MET A 52 NB HEM A 162 2.16 REMARK 500 OH TYR A 25 OE2 GLU A 94 2.17 REMARK 500 OE1 GLU A 94 OE1 GLU A 127 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 SD MET B 52 NC HEM B 162 7556 2.05 REMARK 500 REMARK 500 REMARK: NULL 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),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 108 CB CYS A 108 SG -0.109 REMARK 500 GLU C 146 CB GLU C 146 CG 0.159 REMARK 500 GLU C 146 CG GLU C 146 CD 0.102 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET B 52 CG - SD - CE ANGL. DEV. = -17.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 PHE A 37 58.40 -112.08 REMARK 500 LEU A 65 15.43 -68.08 REMARK 500 ALA A 97 -36.72 -30.02 REMARK 500 SER A 143 -57.60 -134.76 REMARK 500 ILE B 8 26.21 -76.53 REMARK 500 GLU B 9 -19.19 -146.46 REMARK 500 LEU B 71 20.54 -79.07 REMARK 500 ASN B 75 164.28 -49.09 REMARK 500 ARG B 112 31.88 81.50 REMARK 500 ASP B 113 70.80 -100.01 REMARK 500 ILE B 144 30.11 -97.51 REMARK 500 GLU B 146 13.28 -67.46 REMARK 500 LEU C 91 -73.28 -48.80 REMARK 500 ALA C 157 16.52 -64.51 REMARK 500 REMARK 500 REMARK: NULL 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 FE A 163 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 18 OE1 REMARK 620 2 GLU A 51 OE1 58.1 REMARK 620 3 HIS A 54 ND1 51.0 94.4 REMARK 620 4 GLU A 127 OE2 129.6 153.0 109.7 REMARK 620 5 GLU A 127 OE1 119.4 100.2 152.1 52.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 162 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 52 SD REMARK 620 2 HEM A 162 NA 96.5 REMARK 620 3 HEM A 162 NB 62.6 86.3 REMARK 620 4 HEM A 162 NC 75.2 171.2 92.0 REMARK 620 5 HEM A 162 ND 106.0 84.8 164.7 94.9 REMARK 620 6 MET C 52 SD 142.2 106.1 88.5 82.4 105.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 163 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 18 OE2 REMARK 620 2 GLU B 51 OE2 72.6 REMARK 620 3 HIS B 54 ND1 92.2 85.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 162 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 52 SD REMARK 620 2 HEM B 162 NA 89.5 REMARK 620 3 HEM B 162 NB 73.1 94.3 REMARK 620 4 HEM B 162 NC 92.1 173.9 91.8 REMARK 620 5 HEM B 162 ND 100.5 81.4 172.4 92.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE C 162 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 18 OE1 REMARK 620 2 GLU C 18 OE2 55.3 REMARK 620 3 GLU C 51 OE1 99.5 96.9 REMARK 620 4 GLU C 127 OE1 136.7 81.8 78.1 REMARK 620 5 GLU C 127 OE2 139.3 105.0 119.4 51.3 REMARK 620 N 1 2 3 4 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 162 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 162 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE C 162 DBREF 3GVY A 1 161 UNP Q3J696 Q3J696_RHOS4 1 161 DBREF 3GVY B 1 161 UNP Q3J696 Q3J696_RHOS4 1 161 DBREF 3GVY C 1 161 UNP Q3J696 Q3J696_RHOS4 1 161 SEQRES 1 A 161 MET GLN GLY ASP ALA LYS VAL ILE GLU TYR LEU ASN ALA SEQRES 2 A 161 ALA LEU ARG SER GLU LEU THR ALA VAL SER GLN TYR TRP SEQRES 3 A 161 LEU HIS TYR ARG LEU GLN GLU ASP TRP GLY PHE GLY SER SEQRES 4 A 161 ILE ALA HIS LYS SER ARG LYS GLU SER ILE GLU GLU MET SEQRES 5 A 161 HIS HIS ALA ASP LYS LEU ILE GLN ARG ILE ILE PHE LEU SEQRES 6 A 161 GLY GLY HIS PRO ASN LEU GLN ARG LEU ASN PRO LEU ARG SEQRES 7 A 161 ILE GLY GLN THR LEU ARG GLU THR LEU ASP ALA ASP LEU SEQRES 8 A 161 ALA ALA GLU HIS ASP ALA ARG THR LEU TYR ILE GLU ALA SEQRES 9 A 161 ARG ASP HIS CYS GLU LYS VAL ARG ASP TYR PRO SER LYS SEQRES 10 A 161 MET LEU PHE GLU GLU LEU ILE ALA ASP GLU GLU GLY HIS SEQRES 11 A 161 ILE ASP TYR LEU GLU THR GLN ILE ASP LEU MET GLY SER SEQRES 12 A 161 ILE GLY GLU GLN ASN TYR GLY MET LEU ASN ALA LYS PRO SEQRES 13 A 161 ALA ASP GLU ALA GLU SEQRES 1 B 161 MET GLN GLY ASP ALA LYS VAL ILE GLU TYR LEU ASN ALA SEQRES 2 B 161 ALA LEU ARG SER GLU LEU THR ALA VAL SER GLN TYR TRP SEQRES 3 B 161 LEU HIS TYR ARG LEU GLN GLU ASP TRP GLY PHE GLY SER SEQRES 4 B 161 ILE ALA HIS LYS SER ARG LYS GLU SER ILE GLU GLU MET SEQRES 5 B 161 HIS HIS ALA ASP LYS LEU ILE GLN ARG ILE ILE PHE LEU SEQRES 6 B 161 GLY GLY HIS PRO ASN LEU GLN ARG LEU ASN PRO LEU ARG SEQRES 7 B 161 ILE GLY GLN THR LEU ARG GLU THR LEU ASP ALA ASP LEU SEQRES 8 B 161 ALA ALA GLU HIS ASP ALA ARG THR LEU TYR ILE GLU ALA SEQRES 9 B 161 ARG ASP HIS CYS GLU LYS VAL ARG ASP TYR PRO SER LYS SEQRES 10 B 161 MET LEU PHE GLU GLU LEU ILE ALA ASP GLU GLU GLY HIS SEQRES 11 B 161 ILE ASP TYR LEU GLU THR GLN ILE ASP LEU MET GLY SER SEQRES 12 B 161 ILE GLY GLU GLN ASN TYR GLY MET LEU ASN ALA LYS PRO SEQRES 13 B 161 ALA ASP GLU ALA GLU SEQRES 1 C 161 MET GLN GLY ASP ALA LYS VAL ILE GLU TYR LEU ASN ALA SEQRES 2 C 161 ALA LEU ARG SER GLU LEU THR ALA VAL SER GLN TYR TRP SEQRES 3 C 161 LEU HIS TYR ARG LEU GLN GLU ASP TRP GLY PHE GLY SER SEQRES 4 C 161 ILE ALA HIS LYS SER ARG LYS GLU SER ILE GLU GLU MET SEQRES 5 C 161 HIS HIS ALA ASP LYS LEU ILE GLN ARG ILE ILE PHE LEU SEQRES 6 C 161 GLY GLY HIS PRO ASN LEU GLN ARG LEU ASN PRO LEU ARG SEQRES 7 C 161 ILE GLY GLN THR LEU ARG GLU THR LEU ASP ALA ASP LEU SEQRES 8 C 161 ALA ALA GLU HIS ASP ALA ARG THR LEU TYR ILE GLU ALA SEQRES 9 C 161 ARG ASP HIS CYS GLU LYS VAL ARG ASP TYR PRO SER LYS SEQRES 10 C 161 MET LEU PHE GLU GLU LEU ILE ALA ASP GLU GLU GLY HIS SEQRES 11 C 161 ILE ASP TYR LEU GLU THR GLN ILE ASP LEU MET GLY SER SEQRES 12 C 161 ILE GLY GLU GLN ASN TYR GLY MET LEU ASN ALA LYS PRO SEQRES 13 C 161 ALA ASP GLU ALA GLU HET HEM A 162 43 HET FE A 163 1 HET HEM B 162 43 HET FE B 163 1 HET FE C 162 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM FE FE (III) ION HETSYN HEM HEME FORMUL 4 HEM 2(C34 H32 FE N4 O4) FORMUL 5 FE 3(FE 3+) HELIX 1 1 ASP A 4 TRP A 35 1 32 HELIX 2 2 SER A 39 LEU A 65 1 27 HELIX 3 3 THR A 82 GLU A 109 1 28 HELIX 4 4 ASP A 113 MET A 118 1 6 HELIX 5 5 LEU A 119 GLY A 145 1 27 HELIX 6 6 GLY A 145 ASN A 153 1 9 HELIX 7 7 LYS B 6 TRP B 35 1 30 HELIX 8 8 PHE B 37 LEU B 65 1 29 HELIX 9 9 THR B 82 ARG B 112 1 31 HELIX 10 10 ASP B 113 ILE B 144 1 32 HELIX 11 11 ILE B 144 ASN B 153 1 10 HELIX 12 12 ASP C 4 GLY C 36 1 33 HELIX 13 13 PHE C 37 LEU C 65 1 29 HELIX 14 14 THR C 82 VAL C 111 1 30 HELIX 15 15 ASP C 113 GLY C 145 1 33 HELIX 16 16 GLN C 147 ASN C 153 1 7 LINK OE1 GLU A 18 FE FE A 163 1555 1555 2.70 LINK OE1 GLU A 51 FE FE A 163 1555 1555 2.72 LINK SD MET A 52 FE HEM A 162 1555 1555 2.10 LINK ND1 HIS A 54 FE FE A 163 1555 1555 2.65 LINK OE2 GLU A 127 FE FE A 163 1555 1555 1.83 LINK OE1 GLU A 127 FE FE A 163 1555 1555 2.74 LINK FE HEM A 162 SD MET C 52 1555 1555 2.00 LINK OE2 GLU B 18 FE FE B 163 1555 1555 2.39 LINK OE2 GLU B 51 FE FE B 163 1555 1555 2.16 LINK SD MET B 52 FE HEM B 162 1555 1555 1.49 LINK ND1 HIS B 54 FE FE B 163 1555 1555 2.27 LINK OE1 GLU C 18 FE FE C 162 1555 1555 2.25 LINK OE2 GLU C 18 FE FE C 162 1555 1555 2.40 LINK OE1 GLU C 51 FE FE C 162 1555 1555 2.51 LINK OE1 GLU C 127 FE FE C 162 1555 1555 2.45 LINK OE2 GLU C 127 FE FE C 162 1555 1555 2.65 SITE 1 AC1 9 LEU A 19 TRP A 26 ARG A 45 MET A 52 SITE 2 AC1 9 HIS A 53 TRP C 26 MET C 52 HIS C 53 SITE 3 AC1 9 ALA C 55 SITE 1 AC2 6 LEU B 19 TRP B 26 ARG B 45 MET B 52 SITE 2 AC2 6 HIS B 53 ALA B 55 SITE 1 AC3 4 GLU B 18 GLU B 51 HIS B 54 GLU B 127 SITE 1 AC4 4 GLU A 18 GLU A 51 HIS A 54 GLU A 127 SITE 1 AC5 4 GLU C 18 GLU C 51 HIS C 54 GLU C 127 CRYST1 160.495 160.495 116.276 90.00 90.00 90.00 I 4 2 2 48 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 0.006231 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006231 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008600 0.00000