HEADER TRANSFERASE/RNA 22-APR-09 3H5Y TITLE NOROVIRUS POLYMERASE+PRIMER/TEMPLATE+CTP COMPLEX AT 6 MM MNCL2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA DEPENDENT RNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.48; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3'; COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: PRIMER RNA; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-R(P*UP*GP*CP*CP*CP*GP*GP*GP*C)-3'; COMPND 13 CHAIN: T; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: TEMPLATE RNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NORWALK VIRUS; SOURCE 3 ORGANISM_TAXID: 11983; SOURCE 4 STRAIN: AST6139/01/SP; SOURCE 5 GENE: POLYMERASE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: XL1-BLUE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-2T; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CHEMICALLY SYNTHESIZED SELF-COMPLEMENTARY RNA SOURCE 14 OLIGONUCLEOTIDE WITH 2-BASE OVERHANG; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 OTHER_DETAILS: CHEMICALLY SYNTHESIZED SELF-COMPLEMENTARY RNA SOURCE 18 OLIGONUCLEOTIDE THAT WAS EXTENDED BY A SINGLE CYTIDINE-5'- SOURCE 19 MONOPHOSPHATE RESIDUE DURING CRYSTALLIZATION KEYWDS CALICIVIRUSES, VIRAL RNA POLYMERASE, HYDROLASE, NUCLEOTIDE-BINDING, KEYWDS 2 NUCLEOTIDYLTRANSFERASE, PROTEASE, RNA REPLICATION, RNA-DIRECTED RNA KEYWDS 3 POLYMERASE, THIOL PROTEASE, TRANSFERASE, TRANSFERASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.F.ZAMYATKIN,F.PARRA,A.MACHIN,P.GROCHULSKI,K.K.S.NG REVDAT 5 06-SEP-23 3H5Y 1 REMARK REVDAT 4 13-OCT-21 3H5Y 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3H5Y 1 VERSN REVDAT 2 30-JUN-09 3H5Y 1 JRNL REVDAT 1 19-MAY-09 3H5Y 0 JRNL AUTH D.F.ZAMYATKIN,F.PARRA,A.MACHIN,P.GROCHULSKI,K.K.NG JRNL TITL BINDING OF 2'-AMINO-2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE TO JRNL TITL 2 NOROVIRUS POLYMERASE INDUCES REARRANGEMENT OF THE ACTIVE JRNL TITL 3 SITE. JRNL REF J.MOL.BIOL. V. 390 10 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19426741 JRNL DOI 10.1016/J.JMB.2009.04.069 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 62607 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3296 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4541 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 239 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3725 REMARK 3 NUCLEIC ACID ATOMS : 344 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 372 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.13000 REMARK 3 B22 (A**2) : -1.97000 REMARK 3 B33 (A**2) : -0.16000 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): 0.117 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.115 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.616 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4265 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5840 ; 1.091 ; 2.088 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 471 ; 4.992 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;33.554 ;23.671 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 661 ;12.942 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;17.726 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 649 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3050 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2373 ; 1.316 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3841 ; 2.223 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1892 ; 2.972 ; 3.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1999 ; 4.375 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3H5Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052733. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.97934 REMARK 200 MONOCHROMATOR : CRYO-COOLED FIRST AND SAGITTALLY REMARK 200 BENT SECOND CRYSTAL OF DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : WHITE BEAM SLITS, DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR (DCM), VERTICALLY REMARK 200 FOCUSING MIRROR (VFM) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65904 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : 0.04400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.62200 REMARK 200 R SYM FOR SHELL (I) : 0.62200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3BSO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 160 G/L PEG 8000, 250 G/L GLYCEROL, REMARK 280 100 MM TRIS-CL, 50 MM KCL, 4 MM MGCL2, 6 MM MNCL2, 14 MM REMARK 280 MERCAPTOETHANOL, 1 G/L CHAPS, PH 7.0, VAPOR DIFFUSION, HANGING REMARK 280 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 37.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.80000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, T 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 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 SER A 4 REMARK 465 ASP A 373 REMARK 465 LYS A 374 REMARK 465 THR A 375 REMARK 465 GLU A 376 REMARK 465 GLY A 377 REMARK 465 LYS A 467 REMARK 465 GLU A 468 REMARK 465 GLY A 469 REMARK 465 GLY A 470 REMARK 465 MET A 471 REMARK 465 ASP A 489 REMARK 465 LEU A 490 REMARK 465 SER A 491 REMARK 465 THR A 492 REMARK 465 TRP A 493 REMARK 465 GLU A 494 REMARK 465 GLY A 495 REMARK 465 ASP A 496 REMARK 465 ARG A 497 REMARK 465 ASN A 498 REMARK 465 LEU A 499 REMARK 465 ALA A 500 REMARK 465 PRO A 501 REMARK 465 SER A 502 REMARK 465 PHE A 503 REMARK 465 VAL A 504 REMARK 465 ASN A 505 REMARK 465 GLU A 506 REMARK 465 ASP A 507 REMARK 465 GLY A 508 REMARK 465 VAL A 509 REMARK 465 GLU A 510 REMARK 465 U P 1 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 ARG A 236 O HOH A 865 1.99 REMARK 500 OP1 C P 5 O3 GOL A 517 2.10 REMARK 500 NZ LYS A 87 O HOH A 660 2.13 REMARK 500 CG ASN A 128 O HOH A 812 2.14 REMARK 500 OE1 GLN A 96 O HOH A 832 2.18 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 ARG A 245 54.46 36.94 REMARK 500 GLU A 465 86.84 -53.21 REMARK 500 PHE A 473 127.81 134.67 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 MN A 514 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 99 OD2 REMARK 620 2 GLU A 205 OE2 94.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 511 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 242 OD1 REMARK 620 2 ASP A 343 OD1 97.6 REMARK 620 3 ASP A 344 OD1 85.0 98.4 REMARK 620 4 CTP A 515 O1A 103.0 81.4 172.0 REMARK 620 5 HOH A 670 O 93.4 163.6 94.7 84.2 REMARK 620 6 G P 8 O3' 168.7 78.6 85.1 87.0 92.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 512 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 242 OD2 REMARK 620 2 TYR A 243 O 87.0 REMARK 620 3 ASP A 343 OD2 89.3 86.7 REMARK 620 4 CTP A 515 O1A 96.2 168.6 82.5 REMARK 620 5 CTP A 515 O2B 173.1 86.7 93.1 90.5 REMARK 620 6 CTP A 515 O3G 87.7 87.6 173.6 103.4 89.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 512 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 513 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 514 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CTP A 515 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 516 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 517 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 518 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL T 509 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BSO RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO CTP REMARK 900 RELATED ID: 3BSN RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO 5-NITROCYTIDINE-TRIPHOSPHATE REMARK 900 RELATED ID: 1SH0 RELATED DB: PDB REMARK 900 SAME PROTEIN IN UNLIGANDED FORM REMARK 900 RELATED ID: 3H5X RELATED DB: PDB REMARK 900 SAME PROTEIN BOUND TO 2'-AMINO-2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE DBREF 3H5Y A 1 510 UNP Q70ET3 Q70ET3_9CALI 329 838 DBREF 3H5Y P 1 8 PDB 3H5Y 3H5Y 1 8 DBREF 3H5Y T 1 9 PDB 3H5Y 3H5Y 1 9 SEQADV 3H5Y SER A 2 UNP Q70ET3 GLY 330 ENGINEERED MUTATION SEQRES 1 A 510 GLY SER ASP SER LYS GLY THR TYR CYS GLY ALA PRO ILE SEQRES 2 A 510 LEU GLY PRO GLY SER ALA PRO LYS LEU SER THR LYS THR SEQRES 3 A 510 LYS PHE TRP ARG SER SER THR ALA PRO LEU PRO PRO GLY SEQRES 4 A 510 THR TYR GLU PRO ALA TYR LEU GLY GLY LYS ASP PRO ARG SEQRES 5 A 510 VAL LYS GLY GLY PRO SER LEU GLN GLN VAL MET ARG ASP SEQRES 6 A 510 GLN LEU LYS PRO PHE THR GLU PRO ARG GLY LYS PRO PRO SEQRES 7 A 510 LYS PRO SER VAL LEU GLU ALA ALA LYS LYS THR ILE ILE SEQRES 8 A 510 ASN VAL LEU GLU GLN THR ILE ASP PRO PRO ASP LYS TRP SEQRES 9 A 510 SER PHE ALA GLN ALA CYS ALA SER LEU ASP LYS THR THR SEQRES 10 A 510 SER SER GLY HIS PRO HIS HIS MET ARG LYS ASN ASP CYS SEQRES 11 A 510 TRP ASN GLY GLU SER PHE THR GLY LYS LEU ALA ASP GLN SEQRES 12 A 510 ALA SER LYS ALA ASN LEU MET PHE GLU GLU GLY LYS ASN SEQRES 13 A 510 MET THR PRO VAL TYR THR GLY ALA LEU LYS ASP GLU LEU SEQRES 14 A 510 VAL LYS THR ASP LYS ILE TYR GLY LYS ILE LYS LYS ARG SEQRES 15 A 510 LEU LEU TRP GLY SER ASP LEU ALA THR MET ILE ARG CYS SEQRES 16 A 510 ALA ARG ALA PHE GLY GLY LEU MET ASP GLU LEU LYS THR SEQRES 17 A 510 HIS CYS VAL THR LEU PRO ILE ARG VAL GLY MET ASN MET SEQRES 18 A 510 ASN GLU ASP GLY PRO ILE ILE PHE GLU ARG HIS SER ARG SEQRES 19 A 510 TYR ARG TYR HIS TYR ASP ALA ASP TYR SER ARG TRP ASP SEQRES 20 A 510 SER THR GLN GLN ARG ALA VAL LEU ALA ALA ALA LEU GLU SEQRES 21 A 510 ILE MET VAL LYS PHE SER SER GLU PRO HIS LEU ALA GLN SEQRES 22 A 510 VAL VAL ALA GLU ASP LEU LEU SER PRO SER VAL VAL ASP SEQRES 23 A 510 VAL GLY ASP PHE THR ILE SER ILE ASN GLU GLY LEU PRO SEQRES 24 A 510 SER GLY VAL PRO CYS THR SER GLN TRP ASN SER ILE ALA SEQRES 25 A 510 HIS TRP LEU LEU THR LEU CYS ALA LEU SER GLU VAL THR SEQRES 26 A 510 ASN LEU SER PRO ASP ILE ILE GLN ALA ASN SER LEU PHE SEQRES 27 A 510 SER PHE TYR GLY ASP ASP GLU ILE VAL SER THR ASP ILE SEQRES 28 A 510 LYS LEU ASP PRO GLU LYS LEU THR ALA LYS LEU LYS GLU SEQRES 29 A 510 TYR GLY LEU LYS PRO THR ARG PRO ASP LYS THR GLU GLY SEQRES 30 A 510 PRO LEU VAL ILE SER GLU ASP LEU ASN GLY LEU THR PHE SEQRES 31 A 510 LEU ARG ARG THR VAL THR ARG ASP PRO ALA GLY TRP PHE SEQRES 32 A 510 GLY LYS LEU GLU GLN SER SER ILE LEU ARG GLN MET TYR SEQRES 33 A 510 TRP THR ARG GLY PRO ASN HIS GLU ASP PRO SER GLU THR SEQRES 34 A 510 MET ILE PRO HIS SER GLN ARG PRO ILE GLN LEU MET SER SEQRES 35 A 510 LEU LEU GLY GLU ALA ALA LEU HIS GLY PRO ALA PHE TYR SEQRES 36 A 510 SER LYS ILE SER LYS LEU VAL ILE ALA GLU LEU LYS GLU SEQRES 37 A 510 GLY GLY MET ASP PHE TYR VAL PRO ARG GLN GLU PRO MET SEQRES 38 A 510 PHE ARG TRP MET ARG PHE SER ASP LEU SER THR TRP GLU SEQRES 39 A 510 GLY ASP ARG ASN LEU ALA PRO SER PHE VAL ASN GLU ASP SEQRES 40 A 510 GLY VAL GLU SEQRES 1 P 8 U G C C C G G G SEQRES 1 T 9 U G C C C G G G C HET MN A 511 1 HET MN A 512 1 HET MN A 513 1 HET MN A 514 1 HET CTP A 515 29 HET GOL A 516 6 HET GOL A 517 6 HET GOL A 518 6 HET GOL T 509 6 HETNAM MN MANGANESE (II) ION HETNAM CTP CYTIDINE-5'-TRIPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 MN 4(MN 2+) FORMUL 8 CTP C9 H16 N3 O14 P3 FORMUL 9 GOL 4(C3 H8 O3) FORMUL 13 HOH *372(H2 O) HELIX 1 1 SER A 58 GLU A 72 1 15 HELIX 2 2 LYS A 79 ILE A 98 1 20 HELIX 3 3 SER A 105 LEU A 113 1 9 HELIX 4 4 ARG A 126 TRP A 131 5 6 HELIX 5 5 THR A 137 GLY A 154 1 18 HELIX 6 6 THR A 172 GLY A 177 1 6 HELIX 7 7 ASP A 188 HIS A 209 1 22 HELIX 8 8 ASN A 220 ARG A 234 1 15 HELIX 9 9 TRP A 246 GLN A 250 5 5 HELIX 10 10 GLN A 251 SER A 266 1 16 HELIX 11 11 GLU A 268 SER A 281 1 14 HELIX 12 12 CYS A 304 ASN A 326 1 23 HELIX 13 13 SER A 328 ASN A 335 1 8 HELIX 14 14 ASP A 354 TYR A 365 1 12 HELIX 15 15 GLU A 407 ARG A 413 1 7 HELIX 16 16 ARG A 436 LEU A 449 1 14 HELIX 17 17 GLY A 451 GLU A 465 1 15 HELIX 18 18 ARG A 477 SER A 488 1 12 SHEET 1 A 6 THR A 7 TYR A 8 0 SHEET 2 A 6 ALA A 11 PRO A 16 -1 O ALA A 11 N TYR A 8 SHEET 3 A 6 PHE A 290 ILE A 294 -1 O THR A 291 N LEU A 14 SHEET 4 A 6 SER A 283 ASP A 286 -1 N VAL A 285 O ILE A 292 SHEET 5 A 6 VAL A 160 LEU A 165 1 N TYR A 161 O VAL A 284 SHEET 6 A 6 LEU A 183 GLY A 186 -1 O LEU A 184 N ALA A 164 SHEET 1 B 2 THR A 26 ARG A 30 0 SHEET 2 B 2 TRP A 417 HIS A 423 -1 O THR A 418 N TRP A 29 SHEET 1 C 2 GLU A 42 PRO A 43 0 SHEET 2 C 2 LEU A 169 VAL A 170 -1 O VAL A 170 N GLU A 42 SHEET 1 D 4 SER A 336 TYR A 341 0 SHEET 2 D 4 ASP A 344 THR A 349 -1 O SER A 348 N LEU A 337 SHEET 3 D 4 TYR A 237 TYR A 243 -1 N TYR A 239 O VAL A 347 SHEET 4 D 4 PRO A 369 THR A 370 -1 O THR A 370 N ASP A 242 SHEET 1 E 3 THR A 389 PHE A 390 0 SHEET 2 E 3 ARG A 393 ASP A 398 -1 O ARG A 393 N PHE A 390 SHEET 3 E 3 GLY A 401 LEU A 406 -1 O PHE A 403 N THR A 396 LINK OD2 ASP A 99 MN MN A 514 1555 1555 2.13 LINK OE2 GLU A 205 MN MN A 514 1555 1555 2.14 LINK OD1 ASP A 242 MN MN A 511 1555 1555 2.15 LINK OD2 ASP A 242 MN MN A 512 1555 1555 2.18 LINK O TYR A 243 MN MN A 512 1555 1555 2.21 LINK OD1 ASP A 343 MN MN A 511 1555 1555 2.14 LINK OD2 ASP A 343 MN MN A 512 1555 1555 2.16 LINK OD1 ASP A 344 MN MN A 511 1555 1555 2.14 LINK MN MN A 511 O1A CTP A 515 1555 1555 2.18 LINK MN MN A 511 O HOH A 670 1555 1555 2.21 LINK MN MN A 511 O3' G P 8 1555 1555 2.27 LINK MN MN A 512 O1A CTP A 515 1555 1555 2.35 LINK MN MN A 512 O2B CTP A 515 1555 1555 2.22 LINK MN MN A 512 O3G CTP A 515 1555 1555 2.16 LINK MN MN A 513 O HOH A 637 1555 1555 2.26 CISPEP 1 HIS A 121 PRO A 122 0 -4.32 SITE 1 AC1 7 ASP A 242 ASP A 343 ASP A 344 MN A 512 SITE 2 AC1 7 CTP A 515 HOH A 670 G P 8 SITE 1 AC2 5 ASP A 242 TYR A 243 ASP A 343 MN A 511 SITE 2 AC2 5 CTP A 515 SITE 1 AC3 4 ALA A 241 ASP A 242 ASP A 344 HOH A 637 SITE 1 AC4 4 ASP A 99 GLU A 205 HIS A 209 ASP A 289 SITE 1 AC5 18 ARG A 182 ASP A 242 TYR A 243 SER A 244 SITE 2 AC5 18 ARG A 245 TRP A 246 ASP A 247 SER A 300 SITE 3 AC5 18 THR A 305 ASN A 309 ASP A 343 MN A 511 SITE 4 AC5 18 MN A 512 HOH A 670 HOH A 778 HOH A 815 SITE 5 AC5 18 G P 8 G T 2 SITE 1 AC6 5 ARG A 30 LEU A 36 ARG A 52 HOH A 635 SITE 2 AC6 5 HOH A 638 SITE 1 AC7 9 PHE A 28 LEU A 169 ARG A 413 GLN A 414 SITE 2 AC7 9 TRP A 417 THR A 418 ARG A 419 C P 5 SITE 3 AC7 9 G P 6 SITE 1 AC8 4 ALA A 256 GLU A 260 GLN A 273 HOH A 681 SITE 1 AC9 5 LYS A 166 G T 2 C T 3 C T 4 SITE 2 AC9 5 HOH T 517 CRYST1 74.200 93.600 96.300 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 0.013477 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010684 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010384 0.00000