HEADER HYDROLASE 23-MAY-07 2Q16 TITLE STRUCTURE OF THE E. COLI INOSINE TRIPHOSPHATE PYROPHOSPHATASE RGDB IN TITLE 2 COMPLEX WITH ITP COMPND MOL_ID: 1; COMPND 2 MOLECULE: HAM1 PROTEIN HOMOLOG; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.6.1.19; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: YGGV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS RP; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15-B-BASED P11 KEYWDS ITP PYROPHOSPHATASE X-RAY STRUCTURE ENZYME MECHANISM SUBSTRATE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.U.SINGER,R.LAM,M.PROUDFOOT,T.SKARINA,A.SAVCHENKO,A.F.YAKUNIN REVDAT 5 21-FEB-24 2Q16 1 REMARK REVDAT 4 20-OCT-21 2Q16 1 REMARK SEQADV REVDAT 3 13-JUL-11 2Q16 1 VERSN REVDAT 2 24-FEB-09 2Q16 1 VERSN REVDAT 1 19-FEB-08 2Q16 0 JRNL AUTH A.SAVCHENKO,M.PROUDFOOT,T.SKARINA,A.SINGER,O.LITVINOVA, JRNL AUTH 2 R.SANISHVILI,G.BROWN,N.CHIRGADZE,A.F.YAKUNIN JRNL TITL MOLECULAR BASIS OF THE ANTIMUTAGENIC ACTIVITY OF THE JRNL TITL 2 HOUSE-CLEANING INOSINE TRIPHOSPHATE PYROPHOSPHATASE RDGB JRNL TITL 3 FROM ESCHERICHIA COLI. JRNL REF J.MOL.BIOL. V. 374 1091 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17976651 JRNL DOI 10.1016/J.JMB.2007.10.012 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 34514 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1813 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2510 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.1760 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.2180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2922 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 410 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 24.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 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): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.965 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3058 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4168 ; 1.678 ; 2.002 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 392 ;10.601 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;32.998 ;24.160 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 491 ;13.263 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;20.060 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 477 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2290 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1487 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2089 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 310 ; 0.208 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 7 ; 0.191 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.152 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 30 ; 0.218 ; 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): 1938 ; 0.833 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3095 ; 1.502 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1145 ; 2.518 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1072 ; 4.087 ; 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 : 2 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 1 A 197 REMARK 3 ORIGIN FOR THE GROUP (A): 33.7758 7.5914 11.8241 REMARK 3 T TENSOR REMARK 3 T11: -0.1505 T22: -0.0908 REMARK 3 T33: -0.1058 T12: 0.0046 REMARK 3 T13: 0.0110 T23: 0.0249 REMARK 3 L TENSOR REMARK 3 L11: 1.0008 L22: 2.0608 REMARK 3 L33: 1.8079 L12: -0.0762 REMARK 3 L13: 0.5768 L23: 0.3253 REMARK 3 S TENSOR REMARK 3 S11: 0.0415 S12: -0.0043 S13: 0.0196 REMARK 3 S21: -0.0823 S22: -0.0664 S23: -0.0923 REMARK 3 S31: 0.0573 S32: -0.0873 S33: 0.0248 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 : B 3 B 195 REMARK 3 ORIGIN FOR THE GROUP (A): 33.8441 8.5572 42.9215 REMARK 3 T TENSOR REMARK 3 T11: -0.0748 T22: -0.1141 REMARK 3 T33: -0.1191 T12: 0.0442 REMARK 3 T13: 0.0017 T23: 0.0200 REMARK 3 L TENSOR REMARK 3 L11: 1.7000 L22: 1.6476 REMARK 3 L33: 2.0238 L12: -0.2710 REMARK 3 L13: -1.3069 L23: 0.6599 REMARK 3 S TENSOR REMARK 3 S11: -0.0385 S12: 0.0003 S13: -0.1336 REMARK 3 S21: 0.0461 S22: -0.0229 S23: 0.0292 REMARK 3 S31: 0.0786 S32: -0.0589 S33: 0.0613 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: NULL REMARK 4 REMARK 4 2Q16 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000043019. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97942 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36385 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 500.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.40 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 39.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 17.70 REMARK 200 R MERGE FOR SHELL (I) : 0.55100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4K, 200 MM AMMONIUM SULFATE, REMARK 280 100 MM SODIUM ACETATE, 2% ISO-PROPANOL, 20 MM CALCIUM CHLORIDE, REMARK 280 10MM ITP, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 60.32300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 60.32300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 60.32300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 60.32300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 60.32300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.32300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 60.32300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.32300 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 MSE 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 GLY A 198 REMARK 465 SER A 199 REMARK 465 MSE 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 MSE B 1 REMARK 465 GLN B 2 REMARK 465 ASN B 196 REMARK 465 GLY B 197 REMARK 465 GLY B 198 REMARK 465 SER B 199 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MSE A 1 CG SE CE 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 6306 O HOH A 6398 2.05 REMARK 500 NH1 ARG B 146 O HOH B 216 2.08 REMARK 500 NH2 ARG A 87 O HOH A 6393 2.09 REMARK 500 O HOH A 6277 O HOH A 6279 2.12 REMARK 500 O HOH B 283 O HOH B 306 2.14 REMARK 500 O HOH A 6294 O HOH A 6299 2.15 REMARK 500 O HOH B 325 O HOH B 335 2.18 REMARK 500 OG SER A 178 O HOH A 6334 2.18 REMARK 500 O HOH B 286 O HOH B 292 2.19 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 LEU A 103 -75.16 -5.69 REMARK 500 LEU B 103 -73.77 1.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 102 LEU A 103 128.77 REMARK 500 LEU B 102 LEU B 103 121.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 6245 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ITT A 6246 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ITT B 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K7K RELATED DB: PDB REMARK 900 STRUCTURE OF APO-RGDB REMARK 900 RELATED ID: 2PYU RELATED DB: PDB REMARK 900 RGDB IN COMPLEX WITH IMP REMARK 999 REMARK 999 SEQUENCE REMARK 999 THESE RESIDUES BELONG TO A TEV CLEAVAGE SITE. DBREF 2Q16 A 1 197 UNP P52061 HAM1_ECOLI 1 197 DBREF 2Q16 B 1 197 UNP P52061 HAM1_ECOLI 1 197 SEQADV 2Q16 MSE A -19 UNP P52061 EXPRESSION TAG SEQADV 2Q16 GLY A -18 UNP P52061 EXPRESSION TAG SEQADV 2Q16 SER A -17 UNP P52061 EXPRESSION TAG SEQADV 2Q16 SER A -16 UNP P52061 EXPRESSION TAG SEQADV 2Q16 HIS A -15 UNP P52061 EXPRESSION TAG SEQADV 2Q16 HIS A -14 UNP P52061 EXPRESSION TAG SEQADV 2Q16 HIS A -13 UNP P52061 EXPRESSION TAG SEQADV 2Q16 HIS A -12 UNP P52061 EXPRESSION TAG SEQADV 2Q16 HIS A -11 UNP P52061 EXPRESSION TAG SEQADV 2Q16 HIS A -10 UNP P52061 EXPRESSION TAG SEQADV 2Q16 SER A -9 UNP P52061 EXPRESSION TAG SEQADV 2Q16 SER A -8 UNP P52061 EXPRESSION TAG SEQADV 2Q16 GLY A -7 UNP P52061 EXPRESSION TAG SEQADV 2Q16 LEU A -6 UNP P52061 SEE REMARK 999 SEQADV 2Q16 VAL A -5 UNP P52061 SEE REMARK 999 SEQADV 2Q16 PRO A -4 UNP P52061 SEE REMARK 999 SEQADV 2Q16 ARG A -3 UNP P52061 SEE REMARK 999 SEQADV 2Q16 GLY A -2 UNP P52061 SEE REMARK 999 SEQADV 2Q16 SER A -1 UNP P52061 SEE REMARK 999 SEQADV 2Q16 HIS A 0 UNP P52061 EXPRESSION TAG SEQADV 2Q16 MSE A 1 UNP P52061 MET 1 MODIFIED RESIDUE SEQADV 2Q16 ALA A 69 UNP P52061 ASP 69 ENGINEERED MUTATION SEQADV 2Q16 MSE A 106 UNP P52061 MET 106 MODIFIED RESIDUE SEQADV 2Q16 GLY A 198 UNP P52061 EXPRESSION TAG SEQADV 2Q16 SER A 199 UNP P52061 EXPRESSION TAG SEQADV 2Q16 MSE B -19 UNP P52061 EXPRESSION TAG SEQADV 2Q16 GLY B -18 UNP P52061 EXPRESSION TAG SEQADV 2Q16 SER B -17 UNP P52061 EXPRESSION TAG SEQADV 2Q16 SER B -16 UNP P52061 EXPRESSION TAG SEQADV 2Q16 HIS B -15 UNP P52061 EXPRESSION TAG SEQADV 2Q16 HIS B -14 UNP P52061 EXPRESSION TAG SEQADV 2Q16 HIS B -13 UNP P52061 EXPRESSION TAG SEQADV 2Q16 HIS B -12 UNP P52061 EXPRESSION TAG SEQADV 2Q16 HIS B -11 UNP P52061 EXPRESSION TAG SEQADV 2Q16 HIS B -10 UNP P52061 EXPRESSION TAG SEQADV 2Q16 SER B -9 UNP P52061 EXPRESSION TAG SEQADV 2Q16 SER B -8 UNP P52061 EXPRESSION TAG SEQADV 2Q16 GLY B -7 UNP P52061 EXPRESSION TAG SEQADV 2Q16 LEU B -6 UNP P52061 SEE REMARK 999 SEQADV 2Q16 VAL B -5 UNP P52061 SEE REMARK 999 SEQADV 2Q16 PRO B -4 UNP P52061 SEE REMARK 999 SEQADV 2Q16 ARG B -3 UNP P52061 SEE REMARK 999 SEQADV 2Q16 GLY B -2 UNP P52061 SEE REMARK 999 SEQADV 2Q16 SER B -1 UNP P52061 SEE REMARK 999 SEQADV 2Q16 HIS B 0 UNP P52061 EXPRESSION TAG SEQADV 2Q16 MSE B 1 UNP P52061 MET 1 MODIFIED RESIDUE SEQADV 2Q16 ALA B 69 UNP P52061 ASP 69 ENGINEERED MUTATION SEQADV 2Q16 MSE B 106 UNP P52061 MET 106 MODIFIED RESIDUE SEQADV 2Q16 GLY B 198 UNP P52061 EXPRESSION TAG SEQADV 2Q16 SER B 199 UNP P52061 EXPRESSION TAG SEQRES 1 A 219 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 219 LEU VAL PRO ARG GLY SER HIS MSE GLN LYS VAL VAL LEU SEQRES 3 A 219 ALA THR GLY ASN VAL GLY LYS VAL ARG GLU LEU ALA SER SEQRES 4 A 219 LEU LEU SER ASP PHE GLY LEU ASP ILE VAL ALA GLN THR SEQRES 5 A 219 ASP LEU GLY VAL ASP SER ALA GLU GLU THR GLY LEU THR SEQRES 6 A 219 PHE ILE GLU ASN ALA ILE LEU LYS ALA ARG HIS ALA ALA SEQRES 7 A 219 LYS VAL THR ALA LEU PRO ALA ILE ALA ASP ALA SER GLY SEQRES 8 A 219 LEU ALA VAL ASP VAL LEU GLY GLY ALA PRO GLY ILE TYR SEQRES 9 A 219 SER ALA ARG TYR SER GLY GLU ASP ALA THR ASP GLN LYS SEQRES 10 A 219 ASN LEU GLN LYS LEU LEU GLU THR MSE LYS ASP VAL PRO SEQRES 11 A 219 ASP ASP GLN ARG GLN ALA ARG PHE HIS CYS VAL LEU VAL SEQRES 12 A 219 TYR LEU ARG HIS ALA GLU ASP PRO THR PRO LEU VAL CYS SEQRES 13 A 219 HIS GLY SER TRP PRO GLY VAL ILE THR ARG GLU PRO ALA SEQRES 14 A 219 GLY THR GLY GLY PHE GLY TYR ASP PRO ILE PHE PHE VAL SEQRES 15 A 219 PRO SER GLU GLY LYS THR ALA ALA GLU LEU THR ARG GLU SEQRES 16 A 219 GLU LYS SER ALA ILE SER HIS ARG GLY GLN ALA LEU LYS SEQRES 17 A 219 LEU LEU LEU ASP ALA LEU ARG ASN GLY GLY SER SEQRES 1 B 219 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 219 LEU VAL PRO ARG GLY SER HIS MSE GLN LYS VAL VAL LEU SEQRES 3 B 219 ALA THR GLY ASN VAL GLY LYS VAL ARG GLU LEU ALA SER SEQRES 4 B 219 LEU LEU SER ASP PHE GLY LEU ASP ILE VAL ALA GLN THR SEQRES 5 B 219 ASP LEU GLY VAL ASP SER ALA GLU GLU THR GLY LEU THR SEQRES 6 B 219 PHE ILE GLU ASN ALA ILE LEU LYS ALA ARG HIS ALA ALA SEQRES 7 B 219 LYS VAL THR ALA LEU PRO ALA ILE ALA ASP ALA SER GLY SEQRES 8 B 219 LEU ALA VAL ASP VAL LEU GLY GLY ALA PRO GLY ILE TYR SEQRES 9 B 219 SER ALA ARG TYR SER GLY GLU ASP ALA THR ASP GLN LYS SEQRES 10 B 219 ASN LEU GLN LYS LEU LEU GLU THR MSE LYS ASP VAL PRO SEQRES 11 B 219 ASP ASP GLN ARG GLN ALA ARG PHE HIS CYS VAL LEU VAL SEQRES 12 B 219 TYR LEU ARG HIS ALA GLU ASP PRO THR PRO LEU VAL CYS SEQRES 13 B 219 HIS GLY SER TRP PRO GLY VAL ILE THR ARG GLU PRO ALA SEQRES 14 B 219 GLY THR GLY GLY PHE GLY TYR ASP PRO ILE PHE PHE VAL SEQRES 15 B 219 PRO SER GLU GLY LYS THR ALA ALA GLU LEU THR ARG GLU SEQRES 16 B 219 GLU LYS SER ALA ILE SER HIS ARG GLY GLN ALA LEU LYS SEQRES 17 B 219 LEU LEU LEU ASP ALA LEU ARG ASN GLY GLY SER MODRES 2Q16 MSE A 1 MET SELENOMETHIONINE MODRES 2Q16 MSE A 106 MET SELENOMETHIONINE MODRES 2Q16 MSE B 106 MET SELENOMETHIONINE HET MSE A 1 5 HET MSE A 106 8 HET MSE B 106 8 HET CA A 200 1 HET NA A 201 1 HET NA A 202 1 HET NA A 203 1 HET SO4 A6245 5 HET ITT A6246 31 HET CA B 200 1 HET NA B 201 1 HET NA B 202 1 HET ITT B 203 31 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION HETNAM ITT INOSINE 5'-TRIPHOSPHATE HETSYN ITT INOSINE TRIPHOSPHATE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 3 CA 2(CA 2+) FORMUL 4 NA 5(NA 1+) FORMUL 7 SO4 O4 S 2- FORMUL 8 ITT 2(C10 H15 N4 O14 P3) FORMUL 13 HOH *410(H2 O) HELIX 1 1 ASN A 10 GLY A 25 1 16 HELIX 2 2 THR A 32 GLY A 35 5 4 HELIX 3 3 THR A 45 ALA A 62 1 18 HELIX 4 4 VAL A 76 GLY A 78 5 3 HELIX 5 5 PRO A 81 SER A 85 5 5 HELIX 6 6 THR A 94 MSE A 106 1 13 HELIX 7 7 PRO A 110 GLN A 113 5 4 HELIX 8 8 TYR A 156 PRO A 158 5 3 HELIX 9 9 THR A 168 LEU A 172 5 5 HELIX 10 10 THR A 173 SER A 181 1 9 HELIX 11 11 SER A 181 ASN A 196 1 16 HELIX 12 12 ASN B 10 GLY B 25 1 16 HELIX 13 13 THR B 32 GLY B 35 5 4 HELIX 14 14 THR B 45 ALA B 62 1 18 HELIX 15 15 VAL B 76 GLY B 78 5 3 HELIX 16 16 PRO B 81 SER B 85 5 5 HELIX 17 17 THR B 94 MSE B 106 1 13 HELIX 18 18 PRO B 110 GLN B 113 5 4 HELIX 19 19 TYR B 156 PRO B 158 5 3 HELIX 20 20 THR B 168 LEU B 172 5 5 HELIX 21 21 THR B 173 SER B 181 1 9 HELIX 22 22 SER B 181 ARG B 195 1 15 SHEET 1 A 6 ASP A 27 ALA A 30 0 SHEET 2 A 6 LYS A 3 LEU A 6 1 N VAL A 4 O ASP A 27 SHEET 3 A 6 ALA A 65 VAL A 74 1 O ILE A 66 N VAL A 5 SHEET 4 A 6 GLN A 115 LEU A 125 -1 O ARG A 117 N ALA A 73 SHEET 5 A 6 LEU A 134 ILE A 144 -1 O CYS A 136 N LEU A 122 SHEET 6 A 6 PHE A 160 PHE A 161 -1 O PHE A 161 N VAL A 143 SHEET 1 B 6 ILE B 28 ALA B 30 0 SHEET 2 B 6 VAL B 4 LEU B 6 1 N LEU B 6 O VAL B 29 SHEET 3 B 6 ALA B 65 VAL B 74 1 O ILE B 66 N VAL B 5 SHEET 4 B 6 GLN B 115 LEU B 125 -1 O ARG B 117 N ALA B 73 SHEET 5 B 6 LEU B 134 ILE B 144 -1 O CYS B 136 N LEU B 122 SHEET 6 B 6 PHE B 160 PHE B 161 -1 O PHE B 161 N VAL B 143 CISPEP 1 ALA A 80 PRO A 81 0 -5.57 CISPEP 2 ALA B 80 PRO B 81 0 -2.25 SITE 1 AC1 4 GLU A 41 ITT A6246 HOH A6450 HOH A6455 SITE 1 AC2 5 ASN A 10 ASP A 95 PHE A 154 ITT A6246 SITE 2 AC2 5 HOH A6268 SITE 1 AC3 5 ILE A 83 SER A 85 ALA A 86 ITT A6246 SITE 2 AC3 5 HOH A6372 SITE 1 AC4 2 GLU A 16 SER A 181 SITE 1 AC5 3 ARG A 195 ASP B 75 ARG B 117 SITE 1 AC6 3 GLU B 41 ITT B 203 HOH B 347 SITE 1 AC7 4 ASN B 10 ASP B 95 ITT B 203 HOH B 237 SITE 1 AC8 5 ASP B 95 ASN B 98 TYR B 156 ITT B 203 SITE 2 AC8 5 HOH B 227 SITE 1 AC9 30 THR A 8 GLY A 9 ASN A 10 LYS A 13 SITE 2 AC9 30 GLU A 41 LYS A 53 ASP A 68 ALA A 69 SITE 3 AC9 30 SER A 70 GLY A 71 SER A 85 ALA A 86 SITE 4 AC9 30 PHE A 118 PHE A 154 GLY A 155 TYR A 156 SITE 5 AC9 30 ASP A 157 LYS A 177 HIS A 182 ARG A 183 SITE 6 AC9 30 CA A 200 NA A 201 NA A 202 HOH A6251 SITE 7 AC9 30 HOH A6268 HOH A6274 HOH A6323 HOH A6328 SITE 8 AC9 30 HOH A6450 HOH A6455 SITE 1 BC1 28 THR B 8 GLY B 9 ASN B 10 LYS B 13 SITE 2 BC1 28 GLU B 41 LYS B 53 ASP B 68 ALA B 69 SITE 3 BC1 28 SER B 70 GLY B 71 SER B 85 ALA B 86 SITE 4 BC1 28 PHE B 118 PHE B 154 GLY B 155 TYR B 156 SITE 5 BC1 28 ASP B 157 LYS B 177 HIS B 182 ARG B 183 SITE 6 BC1 28 CA B 200 NA B 201 NA B 202 HOH B 232 SITE 7 BC1 28 HOH B 237 HOH B 264 HOH B 360 HOH B 364 CRYST1 120.646 120.646 66.562 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 0.008289 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008289 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015024 0.00000 HETATM 1 N MSE A 1 39.832 34.044 15.275 1.00 47.84 N HETATM 2 CA MSE A 1 40.984 34.082 16.228 1.00 47.03 C HETATM 3 C MSE A 1 41.415 32.666 16.610 1.00 46.61 C HETATM 4 O MSE A 1 42.257 32.082 15.921 1.00 46.87 O HETATM 5 CB MSE A 1 40.643 34.911 17.468 1.00 47.56 C