HEADER TRANSFERASE 14-SEP-11 3TTD TITLE CRYSTAL STRUCTURE OF E. COLI HYPF WITH AMP-CPP AND CARBAMOYL PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATORY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 92-747; COMPND 5 SYNONYM: HYPF; COMPND 6 EC: 2.1.3.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83334; SOURCE 4 STRAIN: O157; SOURCE 5 GENE: ECS3568, HYPF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T1 KEYWDS ZN FINGER, NUCLEOTIDE BINDING, HYDROGENASE MATURATION FACTOR, HYPE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.PETKUN,R.SHI,Y.LI,M.CYGLER REVDAT 2 28-FEB-24 3TTD 1 REMARK SEQADV LINK REVDAT 1 28-DEC-11 3TTD 0 JRNL AUTH S.PETKUN,R.SHI,Y.LI,A.ASINAS,C.MUNGER,L.ZHANG,M.WACLAWEK, JRNL AUTH 2 B.SOBOH,R.G.SAWERS,M.CYGLER JRNL TITL STRUCTURE OF HYDROGENASE MATURATION PROTEIN HYPF WITH JRNL TITL 2 REACTION INTERMEDIATES SHOWS TWO ACTIVE SITES. JRNL REF STRUCTURE V. 19 1773 2011 JRNL REFN ISSN 0969-2126 JRNL PMID 22153500 JRNL DOI 10.1016/J.STR.2011.09.023 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 33728 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1781 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2158 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.1620 REMARK 3 BIN FREE R VALUE SET COUNT : 123 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4929 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 336 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : 0.92000 REMARK 3 B33 (A**2) : -0.87000 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): 0.241 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.194 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.979 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5100 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6971 ; 1.670 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 656 ; 6.192 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 229 ;35.735 ;23.799 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 773 ;15.676 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;15.284 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 769 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3996 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2375 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3488 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 325 ; 0.171 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 1.420 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 45 ; 0.158 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.196 ; 0.200 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): 3351 ; 1.075 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5220 ; 1.738 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2000 ; 2.856 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1751 ; 4.388 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 101 A 187 REMARK 3 ORIGIN FOR THE GROUP (A): 23.0010 50.1940 9.2770 REMARK 3 T TENSOR REMARK 3 T11: 0.0401 T22: -0.0214 REMARK 3 T33: -0.0518 T12: -0.0060 REMARK 3 T13: 0.0021 T23: 0.0206 REMARK 3 L TENSOR REMARK 3 L11: 0.2417 L22: 1.0111 REMARK 3 L33: 1.4080 L12: 0.0676 REMARK 3 L13: -0.1180 L23: -0.0307 REMARK 3 S TENSOR REMARK 3 S11: 0.0407 S12: 0.0230 S13: 0.0489 REMARK 3 S21: -0.1521 S22: 0.0091 S23: -0.0305 REMARK 3 S31: -0.1696 S32: 0.0715 S33: -0.0498 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 188 A 378 REMARK 3 ORIGIN FOR THE GROUP (A): 14.0740 38.5810 27.4310 REMARK 3 T TENSOR REMARK 3 T11: -0.0296 T22: 0.0137 REMARK 3 T33: -0.0292 T12: 0.0070 REMARK 3 T13: -0.0074 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 0.4309 L22: 0.4171 REMARK 3 L33: 0.5971 L12: -0.1770 REMARK 3 L13: 0.0993 L23: -0.0310 REMARK 3 S TENSOR REMARK 3 S11: 0.0339 S12: -0.0463 S13: 0.0047 REMARK 3 S21: -0.0328 S22: -0.0085 S23: 0.0648 REMARK 3 S31: -0.0238 S32: -0.0118 S33: -0.0253 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 379 A 747 REMARK 3 ORIGIN FOR THE GROUP (A): 23.9180 10.0820 26.1760 REMARK 3 T TENSOR REMARK 3 T11: -0.0313 T22: 0.0496 REMARK 3 T33: -0.0340 T12: -0.0033 REMARK 3 T13: -0.0026 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.0905 L22: 0.1362 REMARK 3 L33: 0.2200 L12: -0.0061 REMARK 3 L13: -0.0899 L23: -0.0749 REMARK 3 S TENSOR REMARK 3 S11: -0.0028 S12: -0.0108 S13: -0.0358 REMARK 3 S21: -0.0133 S22: 0.0047 S23: 0.0132 REMARK 3 S31: -0.0154 S32: 0.0076 S33: -0.0020 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 REMARK 4 REMARK 4 3TTD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067894. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37601 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 100.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 51.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 8.5, 20 MM MAGNESIUM REMARK 280 CHLORIDE, 2.5% W/V ISOPROPANOL, 10% W/V ETHYLENE GLYCOL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 23.22300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 100.31750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.86500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 100.31750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.22300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.86500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLY A 90 REMARK 465 SER A 91 REMARK 465 GLN A 92 REMARK 465 SER A 93 REMARK 465 ALA A 94 REMARK 465 GLY A 95 REMARK 465 GLY A 96 REMARK 465 ALA A 97 REMARK 465 MET A 98 REMARK 465 ASN A 99 REMARK 465 THR A 100 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 852 O HOH A 947 2.01 REMARK 500 O HOH A 36 O HOH A 996 2.03 REMARK 500 O HOH A 929 O HOH A 967 2.17 REMARK 500 OE1 GLN A 683 NH2 ARG A 687 2.18 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 406 CB CYS A 406 SG -0.238 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 137 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 VAL A 152 CG1 - CB - CG2 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG A 707 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 707 NE - CZ - NH2 ANGL. DEV. = -3.1 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 THR A 108 127.98 -39.97 REMARK 500 ARG A 137 -85.02 -131.06 REMARK 500 PRO A 178 30.03 -97.03 REMARK 500 HIS A 193 79.48 38.12 REMARK 500 GLN A 199 -134.14 55.41 REMARK 500 ALA A 247 -46.17 -133.57 REMARK 500 SER A 374 -115.74 -138.22 REMARK 500 PRO A 379 45.08 -103.04 REMARK 500 ALA A 588 55.90 -152.91 REMARK 500 ASP A 642 -108.14 79.95 REMARK 500 PRO A 660 150.96 -47.59 REMARK 500 GLN A 721 -51.04 -141.81 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 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 109 SG REMARK 620 2 CYS A 112 SG 111.7 REMARK 620 3 CYS A 131 SG 103.5 101.9 REMARK 620 4 CYS A 134 SG 113.5 103.6 122.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 159 SG REMARK 620 2 CYS A 162 SG 103.3 REMARK 620 3 CYS A 181 SG 103.7 104.9 REMARK 620 4 CYS A 184 SG 117.0 108.4 118.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 3 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 475 NE2 REMARK 620 2 HIS A 479 NE2 100.0 REMARK 620 3 ASP A 502 OD1 104.2 93.1 REMARK 620 4 ASP A 727 OD1 75.3 93.3 173.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 748 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 52 O REMARK 620 2 TYR A 282 O 85.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 748 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TSP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HYPF REMARK 900 RELATED ID: 3TSQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HYPF WITH ATP AND CARBAMOYL PHOSPHATE REMARK 900 RELATED ID: 3TSU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HYPF WITH AMP-PNP AND CARBAMOYL REMARK 900 PHOSPHATE REMARK 900 RELATED ID: 3TTC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HYPF WITH ADP AND CARBAMOYL PHOSPHATE REMARK 900 RELATED ID: 3TTF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HYPF WITH AMP AND CARBAMOYL PHOSPHATE DBREF 3TTD A 92 747 UNP Q7ABC4 Q7ABC4_ECO57 92 747 SEQADV 3TTD GLY A 90 UNP Q7ABC4 EXPRESSION TAG SEQADV 3TTD SER A 91 UNP Q7ABC4 EXPRESSION TAG SEQADV 3TTD ALA A 571 UNP Q7ABC4 GLN 571 CONFLICT SEQADV 3TTD ALA A 572 UNP Q7ABC4 GLN 572 CONFLICT SEQADV 3TTD ALA A 573 UNP Q7ABC4 GLN 573 CONFLICT SEQRES 1 A 658 GLY SER GLN SER ALA GLY GLY ALA MET ASN THR GLN ILE SEQRES 2 A 658 VAL PRO ASP ALA ALA THR CYS PRO ALA CYS LEU ALA GLU SEQRES 3 A 658 MET ASN THR PRO GLY GLU ARG ARG TYR ARG TYR PRO PHE SEQRES 4 A 658 ILE ASN CYS THR HIS CYS GLY PRO ARG PHE THR ILE ILE SEQRES 5 A 658 ARG ALA MET PRO TYR ASP ARG PRO PHE THR VAL MET ALA SEQRES 6 A 658 ALA PHE PRO LEU CYS PRO ALA CYS ASP LYS GLU TYR ARG SEQRES 7 A 658 ASP PRO LEU ASP ARG ARG PHE HIS ALA GLN PRO VAL ALA SEQRES 8 A 658 CYS PRO GLU CYS GLY PRO TYR LEU GLU TRP VAL SER HIS SEQRES 9 A 658 GLY GLU HIS ALA GLU GLN GLU ALA ALA LEU GLN ALA ALA SEQRES 10 A 658 ILE ALA GLN LEU LYS MET GLY ASN ILE VAL ALA ILE LYS SEQRES 11 A 658 GLY ILE GLY GLY PHE HIS LEU ALA CYS ASP ALA ARG ASN SEQRES 12 A 658 SER ASN ALA VAL ALA THR LEU ARG ALA ARG LYS HIS ARG SEQRES 13 A 658 PRO ALA LYS PRO LEU ALA VAL MET LEU PRO VAL ALA ASP SEQRES 14 A 658 GLY LEU PRO ASP ALA ALA ARG GLN LEU LEU THR THR PRO SEQRES 15 A 658 ALA ALA PRO ILE VAL LEU VAL ASP LYS LYS TYR VAL PRO SEQRES 16 A 658 GLU LEU CYS ASP ASP ILE ALA PRO GLY LEU ASN GLU VAL SEQRES 17 A 658 GLY VAL MET LEU PRO ALA ASN PRO LEU GLN HIS LEU LEU SEQRES 18 A 658 LEU GLN GLU LEU GLN CYS PRO LEU VAL MET THR SER GLY SEQRES 19 A 658 ASN LEU SER GLY LYS PRO PRO ALA ILE SER ASN GLU GLN SEQRES 20 A 658 ALA LEU GLU ASP LEU GLN GLY ILE ALA ASP GLY PHE LEU SEQRES 21 A 658 ILE HIS ASN ARG ASP ILE VAL GLN ARG MET ASP ASP SER SEQRES 22 A 658 VAL VAL ARG GLU SER GLY GLU MET LEU ARG ARG SER ARG SEQRES 23 A 658 GLY TYR VAL PRO ASP ALA LEU ALA LEU PRO PRO GLY PHE SEQRES 24 A 658 LYS ASN VAL PRO PRO VAL LEU CYS LEU GLY ALA ASP LEU SEQRES 25 A 658 LYS ASN THR PHE CYS LEU VAL ARG GLY GLU GLN VAL VAL SEQRES 26 A 658 LEU SER GLN HIS LEU GLY ASP LEU SER ASP ASP GLY ILE SEQRES 27 A 658 GLN THR GLN TRP ARG GLU ALA LEU ARG LEU MET GLN ASN SEQRES 28 A 658 ILE TYR ASN PHE THR PRO GLN TYR VAL VAL HIS ASP ALA SEQRES 29 A 658 HIS PRO GLY TYR VAL SER CYS GLN TRP ALA SER GLU MET SEQRES 30 A 658 ASN LEU PRO THR GLN THR VAL LEU HIS HIS HIS ALA HIS SEQRES 31 A 658 ALA ALA ALA CYS LEU ALA GLU HIS GLN TRP PRO LEU ASP SEQRES 32 A 658 GLY GLY ASP VAL ILE ALA LEU THR LEU ASP GLY ILE GLY SEQRES 33 A 658 MET GLY GLU ASN GLY ALA LEU TRP GLY GLY GLU CYS LEU SEQRES 34 A 658 ARG VAL ASN TYR ARG GLU CYS GLU HIS LEU GLY GLY LEU SEQRES 35 A 658 PRO ALA VAL ALA LEU PRO GLY GLY ASP LEU ALA ALA LYS SEQRES 36 A 658 GLN PRO TRP ARG ASN LEU LEU ALA GLN CYS LEU ARG PHE SEQRES 37 A 658 VAL PRO GLU TRP GLN ASN TYR PRO GLU THR ALA SER VAL SEQRES 38 A 658 ALA ALA ALA ASN TRP SER VAL LEU ALA ARG ALA ILE GLU SEQRES 39 A 658 ARG GLY ILE ASN ALA PRO LEU ALA SER SER CYS GLY ARG SEQRES 40 A 658 LEU PHE ASP ALA VAL ALA ALA ALA LEU GLY CYS ALA PRO SEQRES 41 A 658 ALA THR LEU SER TYR GLU GLY GLU ALA ALA CYS ALA LEU SEQRES 42 A 658 GLU ALA LEU ALA ALA SER CYS ASP GLY VAL THR HIS PRO SEQRES 43 A 658 VAL THR MET PRO ARG VAL ASP ASN GLN LEU ASP LEU ALA SEQRES 44 A 658 THR PHE TRP GLN GLN TRP LEU ASN TRP GLN ALA PRO VAL SEQRES 45 A 658 ASN GLN ARG ALA TRP ALA PHE HIS ASP ALA LEU ALA GLN SEQRES 46 A 658 GLY PHE ALA ALA LEU MET ARG GLU GLN ALA THR MET ARG SEQRES 47 A 658 GLY ILE THR THR LEU VAL PHE SER GLY GLY VAL ILE HIS SEQRES 48 A 658 ASN ARG LEU LEU ARG ALA ARG LEU ALA HIS TYR LEU ALA SEQRES 49 A 658 ASP PHE THR LEU LEU PHE PRO GLN SER LEU PRO ALA GLY SEQRES 50 A 658 ASP GLY GLY LEU SER LEU GLY GLN GLY VAL ILE ALA ALA SEQRES 51 A 658 ALA ARG TRP LEU ALA GLY GLU VAL HET ZN A 1 1 HET ZN A 2 1 HET ZN A 3 1 HET MG A 748 1 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 2 ZN 3(ZN 2+) FORMUL 5 MG MG 2+ FORMUL 6 HOH *336(H2 O) HELIX 1 1 CYS A 109 ASN A 117 1 9 HELIX 2 2 ARG A 137 ILE A 141 5 5 HELIX 3 3 ASP A 147 PHE A 156 5 10 HELIX 4 4 CYS A 159 ASP A 168 1 10 HELIX 5 5 GLN A 199 MET A 212 1 14 HELIX 6 6 ASN A 232 LYS A 243 1 12 HELIX 7 7 PRO A 261 THR A 269 1 9 HELIX 8 8 LYS A 281 VAL A 283 5 3 HELIX 9 9 ASN A 304 GLN A 315 1 12 HELIX 10 10 SER A 333 GLN A 342 1 10 HELIX 11 11 GLY A 426 TYR A 442 1 17 HELIX 12 12 TYR A 457 SER A 464 1 8 HELIX 13 13 LEU A 474 HIS A 487 1 14 HELIX 14 14 GLU A 508 GLY A 510 5 3 HELIX 15 15 GLY A 538 GLN A 545 5 8 HELIX 16 16 PRO A 546 VAL A 558 1 13 HELIX 17 17 GLU A 560 GLU A 566 5 7 HELIX 18 18 THR A 567 ALA A 573 1 7 HELIX 19 19 TRP A 575 GLY A 585 1 11 HELIX 20 20 CYS A 594 GLY A 606 1 13 HELIX 21 21 GLY A 616 SER A 628 1 13 HELIX 22 22 ASP A 646 ASN A 656 1 11 HELIX 23 23 PRO A 660 MET A 686 1 27 HELIX 24 24 GLY A 696 HIS A 700 5 5 HELIX 25 25 ASN A 701 LEU A 712 1 12 HELIX 26 26 GLY A 726 GLY A 728 5 3 HELIX 27 27 GLY A 729 ALA A 744 1 16 SHEET 1 A11 HIS A 196 GLU A 198 0 SHEET 2 A11 LEU A 188 VAL A 191 -1 N TRP A 190 O ALA A 197 SHEET 3 A11 GLY A 347 HIS A 351 -1 O ILE A 350 N GLU A 189 SHEET 4 A11 VAL A 216 LYS A 219 1 N ALA A 217 O LEU A 349 SHEET 5 A11 PHE A 224 ASP A 229 -1 O HIS A 225 N ILE A 218 SHEET 6 A11 LEU A 318 SER A 322 -1 O THR A 321 N LEU A 226 SHEET 7 A11 VAL A 252 MET A 253 -1 N MET A 253 O LEU A 318 SHEET 8 A11 GLU A 296 MET A 300 1 O GLY A 298 N VAL A 252 SHEET 9 A11 ILE A 275 ASP A 279 -1 N VAL A 276 O VAL A 299 SHEET 10 A11 VAL A 363 ARG A 365 1 O VAL A 364 N ILE A 275 SHEET 11 A11 MET A 370 ARG A 372 -1 O LEU A 371 N VAL A 363 SHEET 1 B 6 LEU A 382 ALA A 383 0 SHEET 2 B 6 GLN A 412 LEU A 415 -1 O VAL A 413 N LEU A 382 SHEET 3 B 6 CYS A 406 GLY A 410 -1 N LEU A 407 O VAL A 414 SHEET 4 B 6 VAL A 391 CYS A 396 -1 N VAL A 391 O GLY A 410 SHEET 5 B 6 TYR A 448 ASP A 452 1 O TYR A 448 N LEU A 395 SHEET 6 B 6 THR A 470 VAL A 473 1 O GLN A 471 N HIS A 451 SHEET 1 C 4 CYS A 525 GLY A 530 0 SHEET 2 C 4 LEU A 512 VAL A 520 -1 N CYS A 517 O LEU A 528 SHEET 3 C 4 LEU A 590 SER A 593 1 O SER A 592 N LEU A 512 SHEET 4 C 4 VAL A 534 ALA A 535 -1 N VAL A 534 O ALA A 591 SHEET 1 D 5 CYS A 525 GLY A 530 0 SHEET 2 D 5 LEU A 512 VAL A 520 -1 N CYS A 517 O LEU A 528 SHEET 3 D 5 VAL A 496 MET A 506 -1 N ALA A 498 O LEU A 518 SHEET 4 D 5 THR A 691 SER A 695 1 O VAL A 693 N ILE A 497 SHEET 5 D 5 THR A 716 LEU A 718 1 O THR A 716 N LEU A 692 SHEET 1 E 2 ARG A 640 VAL A 641 0 SHEET 2 E 2 GLN A 644 LEU A 645 -1 O GLN A 644 N VAL A 641 LINK ZN ZN A 1 SG CYS A 109 1555 1555 2.39 LINK ZN ZN A 1 SG CYS A 112 1555 1555 2.27 LINK ZN ZN A 1 SG CYS A 131 1555 1555 2.38 LINK ZN ZN A 1 SG CYS A 134 1555 1555 2.44 LINK ZN ZN A 2 SG CYS A 159 1555 1555 2.53 LINK ZN ZN A 2 SG CYS A 162 1555 1555 2.32 LINK ZN ZN A 2 SG CYS A 181 1555 1555 2.46 LINK ZN ZN A 2 SG CYS A 184 1555 1555 2.26 LINK ZN ZN A 3 NE2 HIS A 475 1555 1555 2.60 LINK ZN ZN A 3 NE2 HIS A 479 1555 1555 2.41 LINK ZN ZN A 3 OD1 ASP A 502 1555 1555 2.43 LINK ZN ZN A 3 OD1 ASP A 727 1555 1555 2.42 LINK O HOH A 52 MG MG A 748 1555 1555 2.60 LINK O TYR A 282 MG MG A 748 1555 1555 2.28 CISPEP 1 MET A 144 PRO A 145 0 -6.25 CISPEP 2 VAL A 378 PRO A 379 0 3.30 SITE 1 AC1 4 CYS A 109 CYS A 112 CYS A 131 CYS A 134 SITE 1 AC2 4 CYS A 159 CYS A 162 CYS A 181 CYS A 184 SITE 1 AC3 6 HOH A 20 HOH A 36 HIS A 475 HIS A 479 SITE 2 AC3 6 ASP A 502 ASP A 727 SITE 1 AC4 6 HOH A 52 HOH A 53 TYR A 282 ASN A 656 SITE 2 AC4 6 GLN A 658 HOH A 760 CRYST1 46.446 77.730 200.635 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021530 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012865 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004984 0.00000