HEADER HYDROLASE 05-JUN-18 6GPE TITLE CRYSTAL STRUCTURE OF THE CSID GLUTARATE HYDROXYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN CSID; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: CSID, GAB, YGAT, B2659, JW5427; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS JELLY ROLL, GLUTARATE HYDROXYLASE, ALPHA-KETOGLUTARATE-DEPENDENT, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.M.WILLIAMS,O.MAYANS,J.S.HARTIG REVDAT 3 07-FEB-24 6GPE 1 REMARK REVDAT 2 08-FEB-23 6GPE 1 REMARK LINK REVDAT 1 12-DEC-18 6GPE 0 JRNL AUTH S.KNORR,M.SINN,D.GALETSKIY,R.M.WILLIAMS,C.WANG,N.MULLER, JRNL AUTH 2 O.MAYANS,D.SCHLEHECK,J.S.HARTIG JRNL TITL WIDESPREAD BACTERIAL LYSINE DEGRADATION PROCEEDING VIA JRNL TITL 2 GLUTARATE AND L-2-HYDROXYGLUTARATE. JRNL REF NAT COMMUN V. 9 5071 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30498244 JRNL DOI 10.1038/S41467-018-07563-6 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 47921 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1437 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.5131 - 4.7379 0.86 4665 145 0.1794 0.1940 REMARK 3 2 4.7379 - 3.7613 0.90 4620 142 0.1420 0.1528 REMARK 3 3 3.7613 - 3.2861 0.89 4547 141 0.1570 0.1769 REMARK 3 4 3.2861 - 2.9857 0.92 4666 143 0.1718 0.1978 REMARK 3 5 2.9857 - 2.7718 0.92 4641 144 0.1784 0.2279 REMARK 3 6 2.7718 - 2.6084 0.93 4695 145 0.1815 0.1802 REMARK 3 7 2.6084 - 2.4778 0.91 4575 142 0.1916 0.2449 REMARK 3 8 2.4778 - 2.3699 0.93 4672 144 0.2008 0.2982 REMARK 3 9 2.3699 - 2.2787 0.94 4711 146 0.2073 0.2523 REMARK 3 10 2.2787 - 2.2001 0.94 4692 145 0.2237 0.2686 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.220 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 4927 REMARK 3 ANGLE : 0.736 6682 REMARK 3 CHIRALITY : 0.040 720 REMARK 3 PLANARITY : 0.004 876 REMARK 3 DIHEDRAL : 8.499 4121 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6GPE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010366. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 158775 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 45.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 23.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2R6S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08 M SODIUM CHLORIDE, 0.012 M REMARK 280 POTASSIUM CHLORIDE, 0.02 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.04 REMARK 280 M SODIUM CACODYLATE TRIHYDRATE PH 6.0, 30% V/V (+/-)-2-METHYL-2, REMARK 280 4-PENTANEDIOL, 0.012 M SPERMINE TETRAHYDROCHLORIDE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 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+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 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 60.60000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 60.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 60.60000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 60.60000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 60.60000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.60000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 60.60000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.60000 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -121.20000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 -60.60000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 -60.60000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 60.60000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 -60.60000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -121.20000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 -60.60000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 -60.60000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 60.60000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 -60.60000 REMARK 350 BIOMT3 4 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 A 731 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 787 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 ALA A 3 REMARK 465 LEU A 4 REMARK 465 THR A 5 REMARK 465 ALA A 6 REMARK 465 VAL A 7 REMARK 465 GLN A 8 REMARK 465 ASN A 9 REMARK 465 ASN A 10 REMARK 465 ALA A 11 REMARK 465 VAL A 12 REMARK 465 ASP A 13 REMARK 465 SER A 14 REMARK 465 GLY A 15 REMARK 465 ASN A 142 REMARK 465 VAL A 143 REMARK 465 ASP A 144 REMARK 465 ASN A 145 REMARK 465 SER A 146 REMARK 465 ASP A 147 REMARK 465 SER A 148 REMARK 465 TYR A 149 REMARK 465 LEU A 150 REMARK 465 ARG A 151 REMARK 465 GLN A 152 REMARK 465 PRO A 153 REMARK 465 PRO A 217 REMARK 465 PRO A 218 REMARK 465 SER A 219 REMARK 465 LYS A 220 REMARK 465 ASN A 221 REMARK 465 VAL A 222 REMARK 465 SER A 223 REMARK 465 LEU A 326 REMARK 465 GLU A 327 REMARK 465 HIS A 328 REMARK 465 HIS A 329 REMARK 465 HIS A 330 REMARK 465 HIS A 331 REMARK 465 HIS A 332 REMARK 465 HIS A 333 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 ALA B 3 REMARK 465 LEU B 4 REMARK 465 THR B 5 REMARK 465 ALA B 6 REMARK 465 VAL B 7 REMARK 465 GLN B 8 REMARK 465 ASN B 9 REMARK 465 ASN B 10 REMARK 465 ALA B 11 REMARK 465 VAL B 12 REMARK 465 ASP B 13 REMARK 465 SER B 14 REMARK 465 GLY B 15 REMARK 465 GLN B 16 REMARK 465 ASP B 17 REMARK 465 VAL B 143 REMARK 465 ASP B 144 REMARK 465 ASN B 145 REMARK 465 SER B 146 REMARK 465 ASP B 147 REMARK 465 SER B 148 REMARK 465 TYR B 149 REMARK 465 LEU B 150 REMARK 465 ARG B 151 REMARK 465 GLN B 152 REMARK 465 PRO B 153 REMARK 465 SER B 219 REMARK 465 LYS B 220 REMARK 465 ASN B 221 REMARK 465 VAL B 222 REMARK 465 SER B 223 REMARK 465 LEU B 326 REMARK 465 GLU B 327 REMARK 465 HIS B 328 REMARK 465 HIS B 329 REMARK 465 HIS B 330 REMARK 465 HIS B 331 REMARK 465 HIS B 332 REMARK 465 HIS B 333 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 17 CB CG OD1 OD2 REMARK 480 LYS A 43 CE NZ REMARK 480 GLN A 55 CD OE1 NE2 REMARK 480 LYS A 141 CG CD CE NZ REMARK 480 ARG A 155 CB CG CD NE CZ NH1 NH2 REMARK 480 ARG A 296 CD NE CZ NH1 NH2 REMARK 480 GLN B 55 CD OE1 NE2 REMARK 480 ARG B 155 CG CD NE CZ NH1 NH2 REMARK 480 ARG B 296 CD NE CZ NH1 NH2 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 LYS A 106 C - N - CA ANGL. DEV. = 15.4 DEGREES REMARK 500 LYS A 106 CG - CD - CE ANGL. DEV. = -19.4 DEGREES REMARK 500 LEU A 303 CA - CB - CG ANGL. DEV. = 15.5 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 GLU A 92 -103.79 -122.25 REMARK 500 ASP A 103 26.84 -161.48 REMARK 500 HIS A 324 -158.76 64.04 REMARK 500 SER B 29 139.81 -170.44 REMARK 500 GLU B 92 -103.35 -122.02 REMARK 500 ASP B 103 26.39 -160.59 REMARK 500 HIS B 324 -158.21 63.46 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 FE2 A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 160 NE2 REMARK 620 2 ASP A 162 OD1 86.8 REMARK 620 3 HIS A 292 NE2 90.9 87.5 REMARK 620 4 HOH A 616 O 170.1 102.3 85.4 REMARK 620 5 HOH A 690 O 82.0 82.6 168.1 103.0 REMARK 620 6 HOH A 706 O 101.9 170.4 96.4 69.4 94.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 160 NE2 REMARK 620 2 ASP B 162 OD1 90.7 REMARK 620 3 HIS B 292 NE2 92.9 93.4 REMARK 620 4 HOH B 595 O 171.2 97.9 84.8 REMARK 620 5 HOH B 733 O 93.5 174.0 90.6 78.0 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 FE2 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE2 B 401 DBREF 6GPE A 1 325 UNP P76621 CSID_ECOLI 1 325 DBREF 6GPE B 1 325 UNP P76621 CSID_ECOLI 1 325 SEQADV 6GPE MET A -19 UNP P76621 INITIATING METHIONINE SEQADV 6GPE GLY A -18 UNP P76621 EXPRESSION TAG SEQADV 6GPE SER A -17 UNP P76621 EXPRESSION TAG SEQADV 6GPE SER A -16 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A -15 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A -14 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A -13 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A -12 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A -11 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A -10 UNP P76621 EXPRESSION TAG SEQADV 6GPE SER A -9 UNP P76621 EXPRESSION TAG SEQADV 6GPE SER A -8 UNP P76621 EXPRESSION TAG SEQADV 6GPE GLY A -7 UNP P76621 EXPRESSION TAG SEQADV 6GPE LEU A -6 UNP P76621 EXPRESSION TAG SEQADV 6GPE VAL A -5 UNP P76621 EXPRESSION TAG SEQADV 6GPE PRO A -4 UNP P76621 EXPRESSION TAG SEQADV 6GPE ARG A -3 UNP P76621 EXPRESSION TAG SEQADV 6GPE GLY A -2 UNP P76621 EXPRESSION TAG SEQADV 6GPE SER A -1 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A 0 UNP P76621 EXPRESSION TAG SEQADV 6GPE LEU A 326 UNP P76621 EXPRESSION TAG SEQADV 6GPE GLU A 327 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A 328 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A 329 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A 330 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A 331 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A 332 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS A 333 UNP P76621 EXPRESSION TAG SEQADV 6GPE MET B -19 UNP P76621 INITIATING METHIONINE SEQADV 6GPE GLY B -18 UNP P76621 EXPRESSION TAG SEQADV 6GPE SER B -17 UNP P76621 EXPRESSION TAG SEQADV 6GPE SER B -16 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B -15 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B -14 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B -13 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B -12 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B -11 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B -10 UNP P76621 EXPRESSION TAG SEQADV 6GPE SER B -9 UNP P76621 EXPRESSION TAG SEQADV 6GPE SER B -8 UNP P76621 EXPRESSION TAG SEQADV 6GPE GLY B -7 UNP P76621 EXPRESSION TAG SEQADV 6GPE LEU B -6 UNP P76621 EXPRESSION TAG SEQADV 6GPE VAL B -5 UNP P76621 EXPRESSION TAG SEQADV 6GPE PRO B -4 UNP P76621 EXPRESSION TAG SEQADV 6GPE ARG B -3 UNP P76621 EXPRESSION TAG SEQADV 6GPE GLY B -2 UNP P76621 EXPRESSION TAG SEQADV 6GPE SER B -1 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B 0 UNP P76621 EXPRESSION TAG SEQADV 6GPE LEU B 326 UNP P76621 EXPRESSION TAG SEQADV 6GPE GLU B 327 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B 328 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B 329 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B 330 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B 331 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B 332 UNP P76621 EXPRESSION TAG SEQADV 6GPE HIS B 333 UNP P76621 EXPRESSION TAG SEQRES 1 A 353 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 353 LEU VAL PRO ARG GLY SER HIS MET ASN ALA LEU THR ALA SEQRES 3 A 353 VAL GLN ASN ASN ALA VAL ASP SER GLY GLN ASP TYR SER SEQRES 4 A 353 GLY PHE THR LEU THR PRO SER ALA GLN SER PRO ARG LEU SEQRES 5 A 353 LEU GLU LEU THR PHE THR GLU GLN THR THR LYS GLN PHE SEQRES 6 A 353 LEU GLU GLN VAL ALA GLU TRP PRO VAL GLN ALA LEU GLU SEQRES 7 A 353 TYR LYS SER PHE LEU ARG PHE ARG VAL ALA LYS ILE LEU SEQRES 8 A 353 ASP ASP LEU CYS ALA ASN GLN LEU GLN PRO LEU LEU LEU SEQRES 9 A 353 LYS THR LEU LEU ASN ARG ALA GLU GLY ALA LEU LEU ILE SEQRES 10 A 353 ASN ALA VAL GLY VAL ASP ASP VAL LYS GLN ALA ASP GLU SEQRES 11 A 353 MET VAL LYS LEU ALA THR ALA VAL ALA HIS LEU ILE GLY SEQRES 12 A 353 ARG SER ASN PHE ASP ALA MET SER GLY GLN TYR TYR ALA SEQRES 13 A 353 ARG PHE VAL VAL LYS ASN VAL ASP ASN SER ASP SER TYR SEQRES 14 A 353 LEU ARG GLN PRO HIS ARG VAL MET GLU LEU HIS ASN ASP SEQRES 15 A 353 GLY THR TYR VAL GLU GLU ILE THR ASP TYR VAL LEU MET SEQRES 16 A 353 MET LYS ILE ASP GLU GLN ASN MET GLN GLY GLY ASN SER SEQRES 17 A 353 LEU LEU LEU HIS LEU ASP ASP TRP GLU HIS LEU ASP ASN SEQRES 18 A 353 TYR PHE ARG HIS PRO LEU ALA ARG ARG PRO MET ARG PHE SEQRES 19 A 353 ALA ALA PRO PRO SER LYS ASN VAL SER LYS ASP VAL PHE SEQRES 20 A 353 HIS PRO VAL PHE ASP VAL ASP GLN GLN GLY ARG PRO VAL SEQRES 21 A 353 MET ARG TYR ILE ASP GLN PHE VAL GLN PRO LYS ASP PHE SEQRES 22 A 353 GLU GLU GLY VAL TRP LEU SER GLU LEU SER ASP ALA ILE SEQRES 23 A 353 GLU THR SER LYS GLY ILE LEU SER VAL PRO VAL PRO VAL SEQRES 24 A 353 GLY LYS PHE LEU LEU ILE ASN ASN LEU PHE TRP LEU HIS SEQRES 25 A 353 GLY ARG ASP ARG PHE THR PRO HIS PRO ASP LEU ARG ARG SEQRES 26 A 353 GLU LEU MET ARG GLN ARG GLY TYR PHE ALA TYR ALA SER SEQRES 27 A 353 ASN HIS TYR GLN THR HIS GLN LEU GLU HIS HIS HIS HIS SEQRES 28 A 353 HIS HIS SEQRES 1 B 353 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 353 LEU VAL PRO ARG GLY SER HIS MET ASN ALA LEU THR ALA SEQRES 3 B 353 VAL GLN ASN ASN ALA VAL ASP SER GLY GLN ASP TYR SER SEQRES 4 B 353 GLY PHE THR LEU THR PRO SER ALA GLN SER PRO ARG LEU SEQRES 5 B 353 LEU GLU LEU THR PHE THR GLU GLN THR THR LYS GLN PHE SEQRES 6 B 353 LEU GLU GLN VAL ALA GLU TRP PRO VAL GLN ALA LEU GLU SEQRES 7 B 353 TYR LYS SER PHE LEU ARG PHE ARG VAL ALA LYS ILE LEU SEQRES 8 B 353 ASP ASP LEU CYS ALA ASN GLN LEU GLN PRO LEU LEU LEU SEQRES 9 B 353 LYS THR LEU LEU ASN ARG ALA GLU GLY ALA LEU LEU ILE SEQRES 10 B 353 ASN ALA VAL GLY VAL ASP ASP VAL LYS GLN ALA ASP GLU SEQRES 11 B 353 MET VAL LYS LEU ALA THR ALA VAL ALA HIS LEU ILE GLY SEQRES 12 B 353 ARG SER ASN PHE ASP ALA MET SER GLY GLN TYR TYR ALA SEQRES 13 B 353 ARG PHE VAL VAL LYS ASN VAL ASP ASN SER ASP SER TYR SEQRES 14 B 353 LEU ARG GLN PRO HIS ARG VAL MET GLU LEU HIS ASN ASP SEQRES 15 B 353 GLY THR TYR VAL GLU GLU ILE THR ASP TYR VAL LEU MET SEQRES 16 B 353 MET LYS ILE ASP GLU GLN ASN MET GLN GLY GLY ASN SER SEQRES 17 B 353 LEU LEU LEU HIS LEU ASP ASP TRP GLU HIS LEU ASP ASN SEQRES 18 B 353 TYR PHE ARG HIS PRO LEU ALA ARG ARG PRO MET ARG PHE SEQRES 19 B 353 ALA ALA PRO PRO SER LYS ASN VAL SER LYS ASP VAL PHE SEQRES 20 B 353 HIS PRO VAL PHE ASP VAL ASP GLN GLN GLY ARG PRO VAL SEQRES 21 B 353 MET ARG TYR ILE ASP GLN PHE VAL GLN PRO LYS ASP PHE SEQRES 22 B 353 GLU GLU GLY VAL TRP LEU SER GLU LEU SER ASP ALA ILE SEQRES 23 B 353 GLU THR SER LYS GLY ILE LEU SER VAL PRO VAL PRO VAL SEQRES 24 B 353 GLY LYS PHE LEU LEU ILE ASN ASN LEU PHE TRP LEU HIS SEQRES 25 B 353 GLY ARG ASP ARG PHE THR PRO HIS PRO ASP LEU ARG ARG SEQRES 26 B 353 GLU LEU MET ARG GLN ARG GLY TYR PHE ALA TYR ALA SER SEQRES 27 B 353 ASN HIS TYR GLN THR HIS GLN LEU GLU HIS HIS HIS HIS SEQRES 28 B 353 HIS HIS HET FE2 A 401 1 HET FE2 B 401 1 HETNAM FE2 FE (II) ION FORMUL 3 FE2 2(FE 2+) FORMUL 5 HOH *519(H2 O) HELIX 1 AA1 THR A 38 VAL A 49 1 12 HELIX 2 AA2 PRO A 53 LYS A 60 1 8 HELIX 3 AA3 SER A 61 CYS A 75 1 15 HELIX 4 AA4 GLN A 78 ASN A 89 1 12 HELIX 5 AA5 ASP A 104 LYS A 106 5 3 HELIX 6 AA6 GLN A 107 ILE A 122 1 16 HELIX 7 AA7 ASP A 194 TRP A 196 5 3 HELIX 8 AA8 HIS A 198 ARG A 204 1 7 HELIX 9 AA9 HIS A 205 ARG A 210 5 6 HELIX 10 AB1 ASP A 252 THR A 268 1 17 HELIX 11 AB2 THR B 38 VAL B 49 1 12 HELIX 12 AB3 PRO B 53 LYS B 60 1 8 HELIX 13 AB4 SER B 61 CYS B 75 1 15 HELIX 14 AB5 GLN B 78 ASN B 89 1 12 HELIX 15 AB6 ASP B 104 LYS B 106 5 3 HELIX 16 AB7 GLN B 107 HIS B 120 1 14 HELIX 17 AB8 ASP B 194 TRP B 196 5 3 HELIX 18 AB9 HIS B 198 ARG B 204 1 7 HELIX 19 AC1 HIS B 205 ARG B 210 5 6 HELIX 20 AC2 ASP B 252 THR B 268 1 17 SHEET 1 AA1 7 PHE A 21 PRO A 25 0 SHEET 2 AA1 7 LEU A 32 PHE A 37 -1 O GLU A 34 N THR A 24 SHEET 3 AA1 7 ALA A 94 ALA A 99 1 O ASN A 98 N PHE A 37 SHEET 4 AA1 7 PHE A 282 ASN A 286 -1 O PHE A 282 N ILE A 97 SHEET 5 AA1 7 TYR A 172 GLN A 181 -1 N MET A 175 O LEU A 283 SHEET 6 AA1 7 ARG A 304 PHE A 314 -1 O MET A 308 N MET A 176 SHEET 7 AA1 7 GLY A 123 SER A 125 -1 N ARG A 124 O TYR A 313 SHEET 1 AA2 7 PHE A 21 PRO A 25 0 SHEET 2 AA2 7 LEU A 32 PHE A 37 -1 O GLU A 34 N THR A 24 SHEET 3 AA2 7 ALA A 94 ALA A 99 1 O ASN A 98 N PHE A 37 SHEET 4 AA2 7 PHE A 282 ASN A 286 -1 O PHE A 282 N ILE A 97 SHEET 5 AA2 7 TYR A 172 GLN A 181 -1 N MET A 175 O LEU A 283 SHEET 6 AA2 7 ARG A 304 PHE A 314 -1 O MET A 308 N MET A 176 SHEET 7 AA2 7 ALA A 136 VAL A 140 -1 N VAL A 140 O ARG A 305 SHEET 1 AA3 4 MET A 157 HIS A 160 0 SHEET 2 AA3 4 TRP A 290 ARG A 294 -1 O ARG A 294 N MET A 157 SHEET 3 AA3 4 SER A 188 HIS A 192 -1 N LEU A 191 O LEU A 291 SHEET 4 AA3 4 LEU A 273 VAL A 275 -1 O LEU A 273 N LEU A 190 SHEET 1 AA4 3 VAL A 226 HIS A 228 0 SHEET 2 AA4 3 MET A 212 PHE A 214 -1 N PHE A 214 O VAL A 226 SHEET 3 AA4 3 VAL A 248 GLN A 249 -1 O GLN A 249 N ARG A 213 SHEET 1 AA5 2 PHE A 231 VAL A 233 0 SHEET 2 AA5 2 PRO A 239 MET A 241 -1 O VAL A 240 N ASP A 232 SHEET 1 AA6 7 PHE B 21 PRO B 25 0 SHEET 2 AA6 7 LEU B 32 PHE B 37 -1 O GLU B 34 N THR B 24 SHEET 3 AA6 7 ALA B 94 ALA B 99 1 O LEU B 96 N LEU B 33 SHEET 4 AA6 7 PHE B 282 ASN B 286 -1 O PHE B 282 N ILE B 97 SHEET 5 AA6 7 TYR B 172 GLN B 181 -1 N MET B 175 O LEU B 283 SHEET 6 AA6 7 ARG B 304 PHE B 314 -1 O MET B 308 N MET B 176 SHEET 7 AA6 7 GLY B 123 SER B 125 -1 N ARG B 124 O TYR B 313 SHEET 1 AA7 7 PHE B 21 PRO B 25 0 SHEET 2 AA7 7 LEU B 32 PHE B 37 -1 O GLU B 34 N THR B 24 SHEET 3 AA7 7 ALA B 94 ALA B 99 1 O LEU B 96 N LEU B 33 SHEET 4 AA7 7 PHE B 282 ASN B 286 -1 O PHE B 282 N ILE B 97 SHEET 5 AA7 7 TYR B 172 GLN B 181 -1 N MET B 175 O LEU B 283 SHEET 6 AA7 7 ARG B 304 PHE B 314 -1 O MET B 308 N MET B 176 SHEET 7 AA7 7 ALA B 136 LYS B 141 -1 N VAL B 140 O ARG B 305 SHEET 1 AA8 4 MET B 157 HIS B 160 0 SHEET 2 AA8 4 TRP B 290 ARG B 294 -1 O ARG B 294 N MET B 157 SHEET 3 AA8 4 SER B 188 HIS B 192 -1 N LEU B 191 O LEU B 291 SHEET 4 AA8 4 LEU B 273 VAL B 275 -1 O LEU B 273 N LEU B 190 SHEET 1 AA9 3 VAL B 226 HIS B 228 0 SHEET 2 AA9 3 MET B 212 PHE B 214 -1 N PHE B 214 O VAL B 226 SHEET 3 AA9 3 VAL B 248 GLN B 249 -1 O GLN B 249 N ARG B 213 SHEET 1 AB1 2 PHE B 231 VAL B 233 0 SHEET 2 AB1 2 PRO B 239 MET B 241 -1 O VAL B 240 N ASP B 232 LINK NE2 HIS A 160 FE FE2 A 401 1555 1555 2.47 LINK OD1 ASP A 162 FE FE2 A 401 1555 1555 2.42 LINK NE2 HIS A 292 FE FE2 A 401 1555 1555 2.45 LINK FE FE2 A 401 O HOH A 616 1555 1555 2.24 LINK FE FE2 A 401 O HOH A 690 1555 1555 2.80 LINK FE FE2 A 401 O HOH A 706 1555 1555 2.62 LINK NE2 HIS B 160 FE FE2 B 401 1555 1555 2.45 LINK OD1 ASP B 162 FE FE2 B 401 1555 1555 2.41 LINK NE2 HIS B 292 FE FE2 B 401 1555 1555 2.43 LINK FE FE2 B 401 O HOH B 595 1555 1555 2.65 LINK FE FE2 B 401 O HOH B 733 1555 1555 2.59 SITE 1 AC1 6 HIS A 160 ASP A 162 HIS A 292 HOH A 616 SITE 2 AC1 6 HOH A 690 HOH A 706 SITE 1 AC2 6 HIS B 160 ASP B 162 HIS B 292 HOH B 595 SITE 2 AC2 6 HOH B 713 HOH B 733 CRYST1 121.200 121.200 137.000 90.00 90.00 90.00 P 4 21 2 16 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 0.008251 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008251 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007299 0.00000