HEADER OXIDOREDUCTASE 13-FEB-02 1GVH TITLE THE X-RAY STRUCTURE OF FERRIC ESCHERICHIA COLI FLAVOHEMOGLOBIN REVEALS TITLE 2 AN UNESPECTED GEOMETRY OF THE DISTAL HEME POCKET COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVOHEMOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FLAVOHEMOGLOBIN, DIHYDROPTERIDINE REDUCTASE, HEMOGLOBIN-LIKE COMPND 5 PROTEIN, DIHYDROPTERIDINE REDUCTASE, FERRISIDEROPHORE REDUCTASE B, COMPND 6 NITRIC OXIDE DIOXYGENASE, NOD; COMPND 7 EC: 1.6.99.7 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS OXIDOREDUCTASE, NADP, HEME, FLAVOPROTEIN, FAD, IRON TRANSPOR EXPDTA X-RAY DIFFRACTION AUTHOR A.ILARI,K.A.JOHNSON,A.BONAMORE,A.FARINA,A.BOFFI REVDAT 3 08-MAY-24 1GVH 1 LINK REVDAT 2 24-FEB-09 1GVH 1 VERSN REVDAT 1 06-AUG-02 1GVH 0 JRNL AUTH A.ILARI,A.BONAMORE,A.FARINA,K.A.JOHNSON,A.BOFFI JRNL TITL THE X-RAY STRUCTURE OF FERRIC ESCHERICHIA COLI JRNL TITL 2 FLAVOHEMOGLOBIN REVEALS AN UNEXPECTED GEOMETRY OF THE DISTAL JRNL TITL 3 HEME POCKET JRNL REF J.BIOL.CHEM. V. 277 23725 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11964402 JRNL DOI 10.1074/JBC.M202228200 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 22443 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.247 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 : 3097 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 99 REMARK 3 SOLVENT ATOMS : 191 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 4.190 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 : PROLSQ.PROT REMARK 3 PARAMETER FILE 2 : PARAM19X.HEME REMARK 3 PARAMETER FILE 3 : PARAM.FAD REMARK 3 PARAMETER FILE 4 : PARAM19.SOLV REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X_HEME.PRO REMARK 3 TOPOLOGY FILE 2 : TOPOL.FAD REMARK 3 TOPOLOGY FILE 3 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GVH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1290009427. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.10 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22448 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR 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 (%): 48.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE 0.1 M PH 5.1, PEG 3350 REMARK 280 21-26%, NACL 0.2 M, PH 5.10 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 2 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-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 -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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 0.00000 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PQS 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 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 213.84000 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 213.84000 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 350 BIOMT1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 7 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 213.84000 REMARK 350 BIOMT1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 8 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 9 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 9 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 -1.000000 213.84000 REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 11 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 11 0.000000 0.000000 -1.000000 213.84000 REMARK 350 BIOMT1 12 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 12 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 12 0.000000 0.000000 -1.000000 213.84000 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 O HOH A 2056 O HOH A 2057 2.17 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 HIS A 35 CG HIS A 35 CD2 0.056 REMARK 500 HIS A 101 CG HIS A 101 CD2 0.059 REMARK 500 HIS A 234 CG HIS A 234 CD2 0.062 REMARK 500 HIS A 321 CG HIS A 321 CD2 0.057 REMARK 500 HIS A 393 CG HIS A 393 CD2 0.130 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 ARG A 54 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 TRP A 120 CD1 - CG - CD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 TRP A 120 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 TRP A 149 CD1 - CG - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 TRP A 149 CE2 - CD2 - CG ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 156 NE - CZ - NH1 ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG A 156 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 163 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 TRP A 192 CD1 - CG - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 TRP A 192 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG A 210 NH1 - CZ - NH2 ANGL. DEV. = -8.5 DEGREES REMARK 500 ARG A 210 NE - CZ - NH1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 218 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 TRP A 232 CD1 - CG - CD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 TRP A 232 CE2 - CD2 - CG ANGL. DEV. = -5.4 DEGREES REMARK 500 TRP A 292 CD1 - CG - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 TRP A 292 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 317 NE - CZ - NH1 ANGL. DEV. = -10.2 DEGREES REMARK 500 ARG A 317 NE - CZ - NH2 ANGL. DEV. = 6.6 DEGREES REMARK 500 TRP A 323 CD1 - CG - CD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 TRP A 323 CG - CD1 - NE1 ANGL. DEV. = -6.3 DEGREES REMARK 500 TRP A 323 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 LEU A 396 N - CA - CB ANGL. DEV. = 12.5 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 ASN A 70 32.86 -89.67 REMARK 500 PRO A 185 123.38 -39.65 REMARK 500 LYS A 194 50.47 -165.51 REMARK 500 PRO A 195 179.33 -43.18 REMARK 500 ALA A 247 158.89 -42.83 REMARK 500 HIS A 286 125.94 -35.06 REMARK 500 PHE A 304 18.80 58.76 REMARK 500 CYS A 362 110.97 -163.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 54 0.08 SIDE CHAIN REMARK 500 ARG A 210 0.11 SIDE CHAIN REMARK 500 ARG A 218 0.09 SIDE CHAIN REMARK 500 ARG A 317 0.09 SIDE CHAIN 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 ASP A 3 -10.87 REMARK 500 GLN A 5 11.84 REMARK 500 ILE A 7 -12.40 REMARK 500 LEU A 16 -13.00 REMARK 500 GLU A 19 12.91 REMARK 500 THR A 20 10.98 REMARK 500 LYS A 23 13.22 REMARK 500 MET A 32 12.41 REMARK 500 PRO A 37 10.08 REMARK 500 GLN A 48 -10.31 REMARK 500 ALA A 62 -10.96 REMARK 500 SER A 66 10.55 REMARK 500 SER A 87 11.15 REMARK 500 PHE A 110 12.79 REMARK 500 GLY A 113 -12.00 REMARK 500 LYS A 145 -13.49 REMARK 500 GLY A 151 -12.70 REMARK 500 ILE A 157 10.23 REMARK 500 THR A 161 -11.92 REMARK 500 PRO A 162 13.69 REMARK 500 GLY A 177 -12.77 REMARK 500 ALA A 181 -10.96 REMARK 500 ARG A 184 13.25 REMARK 500 GLY A 190 12.68 REMARK 500 LYS A 194 10.20 REMARK 500 PRO A 195 -13.75 REMARK 500 PHE A 198 -11.47 REMARK 500 GLN A 201 11.71 REMARK 500 LEU A 208 13.01 REMARK 500 THR A 209 14.15 REMARK 500 GLY A 214 -12.04 REMARK 500 ARG A 218 11.35 REMARK 500 ILE A 219 10.06 REMARK 500 HIS A 234 -13.64 REMARK 500 VAL A 239 10.30 REMARK 500 PHE A 252 10.61 REMARK 500 ALA A 257 -10.14 REMARK 500 SER A 266 11.22 REMARK 500 ALA A 267 11.19 REMARK 500 TRP A 292 11.30 REMARK 500 ALA A 295 13.70 REMARK 500 TRP A 323 10.17 REMARK 500 GLU A 340 14.25 REMARK 500 ASP A 344 11.52 REMARK 500 SER A 346 10.41 REMARK 500 PHE A 352 14.83 REMARK 500 CYS A 362 10.19 REMARK 500 GLN A 369 -10.65 REMARK 500 THR A 371 -11.90 REMARK 500 LEU A 378 10.64 REMARK 500 REMARK 500 THIS ENTRY HAS 52 MAIN CHAIN PLANARITY DEVIATIONS. 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 A2002 DISTANCE = 6.21 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 NA A1399 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 40 O REMARK 620 2 PHE A 43 O 88.4 REMARK 620 3 GLN A 201 O 107.6 147.2 REMARK 620 4 GLU A 202 OE1 130.1 104.3 87.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A1398 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 85 NE2 REMARK 620 2 HEM A1398 NA 103.1 REMARK 620 3 HEM A1398 NB 100.9 88.6 REMARK 620 4 HEM A1398 NC 93.0 164.0 88.5 REMARK 620 5 HEM A1398 ND 95.9 91.4 162.8 86.8 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 NA A1399 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A1400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A1397 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A1398 DBREF 1GVH A 1 396 UNP P24232 HMPA_ECOLI 1 396 SEQRES 1 A 396 MET LEU ASP ALA GLN THR ILE ALA THR VAL LYS ALA THR SEQRES 2 A 396 ILE PRO LEU LEU VAL GLU THR GLY PRO LYS LEU THR ALA SEQRES 3 A 396 HIS PHE TYR ASP ARG MET PHE THR HIS ASN PRO GLU LEU SEQRES 4 A 396 LYS GLU ILE PHE ASN MET SER ASN GLN ARG ASN GLY ASP SEQRES 5 A 396 GLN ARG GLU ALA LEU PHE ASN ALA ILE ALA ALA TYR ALA SEQRES 6 A 396 SER ASN ILE GLU ASN LEU PRO ALA LEU LEU PRO ALA VAL SEQRES 7 A 396 GLU LYS ILE ALA GLN LYS HIS THR SER PHE GLN ILE LYS SEQRES 8 A 396 PRO GLU GLN TYR ASN ILE VAL GLY GLU HIS LEU LEU ALA SEQRES 9 A 396 THR LEU ASP GLU MET PHE SER PRO GLY GLN GLU VAL LEU SEQRES 10 A 396 ASP ALA TRP GLY LYS ALA TYR GLY VAL LEU ALA ASN VAL SEQRES 11 A 396 PHE ILE ASN ARG GLU ALA GLU ILE TYR ASN GLU ASN ALA SEQRES 12 A 396 SER LYS ALA GLY GLY TRP GLU GLY THR ARG ASP PHE ARG SEQRES 13 A 396 ILE VAL ALA LYS THR PRO ARG SER ALA LEU ILE THR SER SEQRES 14 A 396 PHE GLU LEU GLU PRO VAL ASP GLY GLY ALA VAL ALA GLU SEQRES 15 A 396 TYR ARG PRO GLY GLN TYR LEU GLY VAL TRP LEU LYS PRO SEQRES 16 A 396 GLU GLY PHE PRO HIS GLN GLU ILE ARG GLN TYR SER LEU SEQRES 17 A 396 THR ARG LYS PRO ASP GLY LYS GLY TYR ARG ILE ALA VAL SEQRES 18 A 396 LYS ARG GLU GLU GLY GLY GLN VAL SER ASN TRP LEU HIS SEQRES 19 A 396 ASN HIS ALA ASN VAL GLY ASP VAL VAL LYS LEU VAL ALA SEQRES 20 A 396 PRO ALA GLY ASP PHE PHE MET ALA VAL ALA ASP ASP THR SEQRES 21 A 396 PRO VAL THR LEU ILE SER ALA GLY VAL GLY GLN THR PRO SEQRES 22 A 396 MET LEU ALA MET LEU ASP THR LEU ALA LYS ALA GLY HIS SEQRES 23 A 396 THR ALA GLN VAL ASN TRP PHE HIS ALA ALA GLU ASN GLY SEQRES 24 A 396 ASP VAL HIS ALA PHE ALA ASP GLU VAL LYS GLU LEU GLY SEQRES 25 A 396 GLN SER LEU PRO ARG PHE THR ALA HIS THR TRP TYR ARG SEQRES 26 A 396 GLN PRO SER GLU ALA ASP ARG ALA LYS GLY GLN PHE ASP SEQRES 27 A 396 SER GLU GLY LEU MET ASP LEU SER LYS LEU GLU GLY ALA SEQRES 28 A 396 PHE SER ASP PRO THR MET GLN PHE TYR LEU CYS GLY PRO SEQRES 29 A 396 VAL GLY PHE MET GLN PHE THR ALA LYS GLN LEU VAL ASP SEQRES 30 A 396 LEU GLY VAL LYS GLN GLU ASN ILE HIS TYR GLU CYS PHE SEQRES 31 A 396 GLY PRO HIS LYS VAL LEU HET FAD A1397 53 HET HEM A1398 43 HET NA A1399 1 HET NA A1400 1 HET CL A1401 1 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETSYN HEM HEME FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 NA 2(NA 1+) FORMUL 6 CL CL 1- FORMUL 7 HOH *191(H2 O) HELIX 1 1 ASP A 3 GLU A 19 1 17 HELIX 2 2 THR A 20 ASN A 36 1 17 HELIX 3 3 PRO A 37 ILE A 42 5 6 HELIX 4 4 GLY A 51 SER A 66 1 16 HELIX 5 5 ASN A 67 ALA A 73 5 7 HELIX 6 6 LEU A 74 PHE A 88 1 15 HELIX 7 7 LYS A 91 SER A 111 1 21 HELIX 8 8 GLY A 113 LYS A 145 1 33 HELIX 9 9 GLY A 227 HIS A 236 1 10 HELIX 10 10 GLN A 271 ALA A 284 1 14 HELIX 11 11 PHE A 304 SER A 314 1 11 HELIX 12 12 SER A 328 GLY A 335 1 8 HELIX 13 13 ASP A 344 LEU A 348 5 5 HELIX 14 14 PRO A 364 LEU A 378 1 15 HELIX 15 15 LYS A 381 GLU A 383 5 3 SHEET 1 AA 6 GLU A 202 SER A 207 0 SHEET 2 AA 6 TYR A 188 LEU A 193 -1 O LEU A 189 N TYR A 206 SHEET 3 AA 6 VAL A 242 ALA A 249 -1 O LYS A 244 N TRP A 192 SHEET 4 AA 6 THR A 152 PRO A 162 -1 O ARG A 153 N LEU A 245 SHEET 5 AA 6 ILE A 167 PRO A 174 -1 O SER A 169 N THR A 161 SHEET 6 AA 6 TYR A 217 LYS A 222 -1 O TYR A 217 N LEU A 172 SHEET 1 AB 6 SER A 339 GLU A 340 0 SHEET 2 AB 6 PHE A 318 TYR A 324 1 O THR A 322 N SER A 339 SHEET 3 AB 6 VAL A 290 ALA A 296 1 O VAL A 290 N THR A 319 SHEET 4 AB 6 VAL A 262 ALA A 267 1 O VAL A 262 N ASN A 291 SHEET 5 AB 6 GLN A 358 CYS A 362 1 O GLN A 358 N THR A 263 SHEET 6 AB 6 ILE A 385 GLU A 388 1 O HIS A 386 N LEU A 361 LINK O LYS A 40 NA NA A1399 1555 1555 2.42 LINK O PHE A 43 NA NA A1399 1555 1555 2.38 LINK NE2 HIS A 85 FE HEM A1398 1555 1555 2.09 LINK O GLN A 201 NA NA A1399 1555 1555 2.44 LINK OE1 GLU A 202 NA NA A1399 1555 1555 2.47 SITE 1 AC1 4 LYS A 40 PHE A 43 GLN A 201 GLU A 202 SITE 1 AC2 5 GLN A 271 HIS A 294 HIS A 302 ALA A 303 SITE 2 AC2 5 HOH A2137 SITE 1 AC3 1 GLY A 51 SITE 1 AC4 27 ASN A 44 SER A 46 GLN A 48 ASN A 50 SITE 2 AC4 27 TYR A 188 ARG A 204 GLN A 205 TYR A 206 SITE 3 AC4 27 SER A 207 ALA A 220 VAL A 221 LYS A 222 SITE 4 AC4 27 GLU A 224 GLU A 225 GLY A 227 GLN A 228 SITE 5 AC4 27 VAL A 229 SER A 230 VAL A 269 THR A 272 SITE 6 AC4 27 GLU A 388 PHE A 390 HOH A2095 HOH A2103 SITE 7 AC4 27 HOH A2187 HOH A2188 HOH A2189 SITE 1 AC5 20 LEU A 39 ASN A 44 GLN A 53 ALA A 56 SITE 2 AC5 20 LEU A 57 ALA A 60 ILE A 61 ILE A 81 SITE 3 AC5 20 LYS A 84 HIS A 85 PHE A 88 ILE A 90 SITE 4 AC5 20 GLN A 94 TYR A 95 VAL A 98 LEU A 127 SITE 5 AC5 20 PRO A 392 HIS A 393 HOH A2190 HOH A2191 CRYST1 164.860 164.860 53.460 90.00 90.00 120.00 P 6 2 2 12 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 0.006066 0.003502 0.000000 0.00000 SCALE2 0.000000 0.007004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018705 0.00000