HEADER TRANSFERASE 07-FEB-17 5N2H TITLE STRUCTURE OF THE E9 DNA POLYMERASE EXONUCLEASE DEFICIENT MUTANT TITLE 2 (D166A+E168A) FROM VACCINIA VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VACCINIA VIRUS E9 DNA POLYMERASE EXO- MUTANT; COMPND 5 EC: 2.7.7.7,3.1.11.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VACCINIA VIRUS COPENHAGEN; SOURCE 3 ORGANISM_TAXID: 10249; SOURCE 4 GENE: POL, E9L; SOURCE 5 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: HIGH FIVE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: UNIDENTIFIED BACULOVIRUS KEYWDS VACCINIA VIRUS, DNA POLYMERASE, PROTEIN-PROTEIN INTERFACE, FAMILY B KEYWDS 2 POLYMERASE, PROCESSIVITY FACTOR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.TARBOURIECH,W.P.BURMEISTER,F.ISENI REVDAT 3 17-JAN-24 5N2H 1 REMARK REVDAT 2 24-OCT-18 5N2H 1 SOURCE REVDAT 1 29-NOV-17 5N2H 0 JRNL AUTH N.TARBOURIECH,C.DUCOURNAU,S.HUTIN,P.J.MAS,P.MAN,E.FOREST, JRNL AUTH 2 D.J.HART,C.N.PEYREFITTE,W.P.BURMEISTER,F.ISENI JRNL TITL THE VACCINIA VIRUS DNA POLYMERASE STRUCTURE PROVIDES JRNL TITL 2 INSIGHTS INTO THE MODE OF PROCESSIVITY FACTOR BINDING. JRNL REF NAT COMMUN V. 8 1455 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29129932 JRNL DOI 10.1038/S41467-017-01542-Z REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 54943 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2805 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) : 2.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3939 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.3470 REMARK 3 BIN FREE R VALUE SET COUNT : 197 REMARK 3 BIN FREE R VALUE : 0.3910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8164 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 214 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.40000 REMARK 3 B22 (A**2) : 1.40000 REMARK 3 B33 (A**2) : -4.56000 REMARK 3 B12 (A**2) : 0.70000 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): 0.337 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.250 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.205 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.231 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8419 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 8000 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11367 ; 1.617 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 18438 ; 0.998 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 998 ; 7.801 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 405 ;36.957 ;23.753 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1519 ;19.211 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 59 ;19.269 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1253 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9337 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1976 ; 0.002 ; 0.020 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): 3995 ; 4.982 ; 7.521 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3994 ; 4.980 ; 7.520 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4989 ; 7.830 ;11.269 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4990 ; 7.829 ;11.270 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4424 ; 5.536 ; 8.039 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 4424 ; 5.534 ; 8.039 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 6378 ; 8.817 ;11.819 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 9247 ;12.579 ;58.302 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 9248 ;12.580 ;58.308 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 : NULL 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 5N2H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003458. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0-6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2724 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57789 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.810 REMARK 200 RESOLUTION RANGE LOW (A) : 57.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5N2G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9-11% PEG 3000, 20-25% GLYCEROL, 100 REMARK 280 MM MES-NAOH PH 6.25, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.49733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 152.99467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 152.99467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 76.49733 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 TOTAL BURIED SURFACE AREA: 2240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 47010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 17.0 KCAL/MOL 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 HIS A 307 REMARK 465 LYS A 308 REMARK 465 GLY A 309 REMARK 465 VAL A 310 REMARK 465 GLY A 311 REMARK 465 GLY A 312 REMARK 465 MET A 313 REMARK 465 LYS A 901 REMARK 465 SER A 902 REMARK 465 ALA A 903 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 NH1 ARG A 519 O HOH A 1201 1.20 REMARK 500 NH2 ARG A 519 O TYR A 679 1.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1251 O HOH A 1251 6555 1.21 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 SER A 51 -84.57 -44.45 REMARK 500 LYS A 96 155.96 -47.37 REMARK 500 ASN A 101 37.72 -140.63 REMARK 500 ILE A 135 -24.59 -141.48 REMARK 500 ASP A 172 -73.33 -111.47 REMARK 500 THR A 255 56.27 -92.45 REMARK 500 PHE A 267 -78.15 -106.54 REMARK 500 GLN A 304 93.59 -161.17 REMARK 500 VAL A 365 -136.21 46.07 REMARK 500 ASP A 377 -71.06 -139.52 REMARK 500 ASP A 400 -54.58 -150.49 REMARK 500 PRO A 422 -157.52 -53.16 REMARK 500 LEU A 424 51.91 -152.75 REMARK 500 PRO A 425 88.60 -62.72 REMARK 500 LYS A 435 -172.58 -46.36 REMARK 500 PHE A 526 140.49 135.80 REMARK 500 TYR A 528 8.83 117.50 REMARK 500 THR A 645 -38.46 -130.63 REMARK 500 ASN A 675 52.08 -91.65 REMARK 500 SER A 680 98.45 -162.08 REMARK 500 ASN A 709 -134.50 53.69 REMARK 500 ASP A 751 -149.39 -128.90 REMARK 500 ASP A 753 23.96 -144.34 REMARK 500 ASN A 785 -131.04 47.32 REMARK 500 LYS A 818 64.19 -119.77 REMARK 500 PRO A 821 -176.22 -49.10 REMARK 500 SER A 829 88.82 -159.01 REMARK 500 GLU A 830 -157.45 -169.08 REMARK 500 THR A 831 168.17 96.75 REMARK 500 ARG A 832 69.81 23.93 REMARK 500 ARG A 833 16.50 87.04 REMARK 500 ASN A 860 -154.92 -101.74 REMARK 500 ASP A 881 -74.60 -91.94 REMARK 500 LEU A 889 -7.90 -57.00 REMARK 500 VAL A 945 -165.76 -122.88 REMARK 500 ASN A 946 98.26 -66.26 REMARK 500 TYR A1004 71.88 -61.68 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 GLY A 281 GLU A 282 -146.83 REMARK 500 LYS A 435 ASP A 436 148.14 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 MES A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 1103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTT A 1106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 1107 DBREF 5N2H A 2 1005 UNP P20509 DPOL_VACCC 2 1005 SEQADV 5N2H GLY A -3 UNP P20509 EXPRESSION TAG SEQADV 5N2H ALA A -2 UNP P20509 EXPRESSION TAG SEQADV 5N2H MET A -1 UNP P20509 EXPRESSION TAG SEQADV 5N2H ASP A 0 UNP P20509 EXPRESSION TAG SEQADV 5N2H PRO A 1 UNP P20509 EXPRESSION TAG SEQADV 5N2H ALA A 166 UNP P20509 ASP 166 ENGINEERED MUTATION SEQADV 5N2H ALA A 168 UNP P20509 GLU 168 ENGINEERED MUTATION SEQRES 1 A 1009 GLY ALA MET ASP PRO ASP VAL ARG CYS ILE ASN TRP PHE SEQRES 2 A 1009 GLU SER HIS GLY GLU ASN ARG PHE LEU TYR LEU LYS SER SEQRES 3 A 1009 ARG CYS ARG ASN GLY GLU THR VAL PHE ILE ARG PHE PRO SEQRES 4 A 1009 HIS TYR PHE TYR TYR VAL VAL THR ASP GLU ILE TYR GLN SEQRES 5 A 1009 SER LEU SER PRO PRO PRO PHE ASN ALA ARG PRO LEU GLY SEQRES 6 A 1009 LYS MET ARG THR ILE ASP ILE ASP GLU THR ILE SER TYR SEQRES 7 A 1009 ASN LEU ASP ILE LYS ASP ARG LYS CYS SER VAL ALA ASP SEQRES 8 A 1009 MET TRP LEU ILE GLU GLU PRO LYS LYS ARG SER ILE GLN SEQRES 9 A 1009 ASN ALA THR MET ASP GLU PHE LEU ASN ILE SER TRP PHE SEQRES 10 A 1009 TYR ILE SER ASN GLY ILE SER PRO ASP GLY CYS TYR SER SEQRES 11 A 1009 LEU ASP GLU GLN TYR LEU THR LYS ILE ASN ASN GLY CYS SEQRES 12 A 1009 TYR HIS CYS ASP ASP PRO ARG ASN CYS PHE ALA LYS LYS SEQRES 13 A 1009 ILE PRO ARG PHE ASP ILE PRO ARG SER TYR LEU PHE LEU SEQRES 14 A 1009 ALA ILE ALA CYS HIS PHE ASP LYS LYS PHE PRO SER VAL SEQRES 15 A 1009 PHE ILE ASN PRO ILE SER HIS THR SER TYR CYS TYR ILE SEQRES 16 A 1009 ASP LEU SER GLY LYS ARG LEU LEU PHE THR LEU ILE ASN SEQRES 17 A 1009 GLU GLU MET LEU THR GLU GLN GLU ILE GLN GLU ALA VAL SEQRES 18 A 1009 ASP ARG GLY CYS LEU ARG ILE GLN SER LEU MET GLU MET SEQRES 19 A 1009 ASP TYR GLU ARG GLU LEU VAL LEU CYS SER GLU ILE VAL SEQRES 20 A 1009 LEU LEU ARG ILE ALA LYS GLN LEU LEU GLU LEU THR PHE SEQRES 21 A 1009 ASP TYR VAL VAL THR PHE ASN GLY HIS ASN PHE ASP LEU SEQRES 22 A 1009 ARG TYR ILE THR ASN ARG LEU GLU LEU LEU THR GLY GLU SEQRES 23 A 1009 LYS ILE ILE PHE ARG SER PRO ASP LYS LYS GLU ALA VAL SEQRES 24 A 1009 HIS LEU CYS ILE TYR GLU ARG ASN GLN SER SER HIS LYS SEQRES 25 A 1009 GLY VAL GLY GLY MET ALA ASN THR THR PHE HIS VAL ASN SEQRES 26 A 1009 ASN ASN ASN GLY THR ILE PHE PHE ASP LEU TYR SER PHE SEQRES 27 A 1009 ILE GLN LYS SER GLU LYS LEU ASP SER TYR LYS LEU ASP SEQRES 28 A 1009 SER ILE SER LYS ASN ALA PHE SER CYS MET GLY LYS VAL SEQRES 29 A 1009 LEU ASN ARG GLY VAL ARG GLU MET THR PHE ILE GLY ASP SEQRES 30 A 1009 ASP THR THR ASP ALA LYS GLY LYS ALA ALA ALA PHE ALA SEQRES 31 A 1009 LYS VAL LEU THR THR GLY ASN TYR VAL THR VAL ASP GLU SEQRES 32 A 1009 ASP ILE ILE CYS LYS VAL ILE ARG LYS ASP ILE TRP GLU SEQRES 33 A 1009 ASN GLY PHE LYS VAL VAL LEU LEU CYS PRO THR LEU PRO SEQRES 34 A 1009 ASN ASP THR TYR LYS LEU SER PHE GLY LYS ASP ASP VAL SEQRES 35 A 1009 ASP LEU ALA GLN MET TYR LYS ASP TYR ASN LEU ASN ILE SEQRES 36 A 1009 ALA LEU ASP MET ALA ARG TYR CYS ILE HIS ASP ALA CYS SEQRES 37 A 1009 LEU CYS GLN TYR LEU TRP GLU TYR TYR GLY VAL GLU THR SEQRES 38 A 1009 LYS THR ASP ALA GLY ALA SER THR TYR VAL LEU PRO GLN SEQRES 39 A 1009 SER MET VAL PHE GLU TYR ARG ALA SER THR VAL ILE LYS SEQRES 40 A 1009 GLY PRO LEU LEU LYS LEU LEU LEU GLU THR LYS THR ILE SEQRES 41 A 1009 LEU VAL ARG SER GLU THR LYS GLN LYS PHE PRO TYR GLU SEQRES 42 A 1009 GLY GLY LYS VAL PHE ALA PRO LYS GLN LYS MET PHE SER SEQRES 43 A 1009 ASN ASN VAL LEU ILE PHE ASP TYR ASN SER LEU TYR PRO SEQRES 44 A 1009 ASN VAL CYS ILE PHE GLY ASN LEU SER PRO GLU THR LEU SEQRES 45 A 1009 VAL GLY VAL VAL VAL SER THR ASN ARG LEU GLU GLU GLU SEQRES 46 A 1009 ILE ASN ASN GLN LEU LEU LEU GLN LYS TYR PRO PRO PRO SEQRES 47 A 1009 ARG TYR ILE THR VAL HIS CYS GLU PRO ARG LEU PRO ASN SEQRES 48 A 1009 LEU ILE SER GLU ILE ALA ILE PHE ASP ARG SER ILE GLU SEQRES 49 A 1009 GLY THR ILE PRO ARG LEU LEU ARG THR PHE LEU ALA GLU SEQRES 50 A 1009 ARG ALA ARG TYR LYS LYS MET LEU LYS GLN ALA THR SER SEQRES 51 A 1009 SER THR GLU LYS ALA ILE TYR ASP SER MET GLN TYR THR SEQRES 52 A 1009 TYR LYS ILE VAL ALA ASN SER VAL TYR GLY LEU MET GLY SEQRES 53 A 1009 PHE ARG ASN SER ALA LEU TYR SER TYR ALA SER ALA LYS SEQRES 54 A 1009 SER CYS THR SER ILE GLY ARG ARG MET ILE LEU TYR LEU SEQRES 55 A 1009 GLU SER VAL LEU ASN GLY ALA GLU LEU SER ASN GLY MET SEQRES 56 A 1009 LEU ARG PHE ALA ASN PRO LEU SER ASN PRO PHE TYR MET SEQRES 57 A 1009 ASP ASP ARG ASP ILE ASN PRO ILE VAL LYS THR SER LEU SEQRES 58 A 1009 PRO ILE ASP TYR ARG PHE ARG PHE ARG SER VAL TYR GLY SEQRES 59 A 1009 ASP THR ASP SER VAL PHE THR GLU ILE ASP SER GLN ASP SEQRES 60 A 1009 VAL ASP LYS SER ILE GLU ILE ALA LYS GLU LEU GLU ARG SEQRES 61 A 1009 LEU ILE ASN ASN ARG VAL LEU PHE ASN ASN PHE LYS ILE SEQRES 62 A 1009 GLU PHE GLU ALA VAL TYR LYS ASN LEU ILE MET GLN SER SEQRES 63 A 1009 LYS LYS LYS TYR THR THR MET LYS TYR SER ALA SER SER SEQRES 64 A 1009 ASN SER LYS SER VAL PRO GLU ARG ILE ASN LYS GLY THR SEQRES 65 A 1009 SER GLU THR ARG ARG ASP VAL SER LYS PHE HIS LYS ASN SEQRES 66 A 1009 MET ILE LYS THR TYR LYS THR ARG LEU SER GLU MET LEU SEQRES 67 A 1009 SER GLU GLY ARG MET ASN SER ASN GLN VAL CYS ILE ASP SEQRES 68 A 1009 ILE LEU ARG SER LEU GLU THR ASP LEU ARG SER GLU PHE SEQRES 69 A 1009 ASP SER ARG SER SER PRO LEU GLU LEU PHE MET LEU SER SEQRES 70 A 1009 ARG MET HIS HIS SER ASN TYR LYS SER ALA ASP ASN PRO SEQRES 71 A 1009 ASN MET TYR LEU VAL THR GLU TYR ASN LYS ASN ASN PRO SEQRES 72 A 1009 GLU THR ILE GLU LEU GLY GLU ARG TYR TYR PHE ALA TYR SEQRES 73 A 1009 ILE CYS PRO ALA ASN VAL PRO TRP THR LYS LYS LEU VAL SEQRES 74 A 1009 ASN ILE LYS THR TYR GLU THR ILE ILE ASP ARG SER PHE SEQRES 75 A 1009 LYS LEU GLY SER ASP GLN ARG ILE PHE TYR GLU VAL TYR SEQRES 76 A 1009 PHE LYS ARG LEU THR SER GLU ILE VAL ASN LEU LEU ASP SEQRES 77 A 1009 ASN LYS VAL LEU CYS ILE SER PHE PHE GLU ARG MET PHE SEQRES 78 A 1009 GLY SER LYS PRO THR PHE TYR GLU HET MES A1101 12 HET MES A1102 12 HET MES A1103 12 HET GOL A1104 6 HET GOL A1105 6 HET DTT A1106 8 HET EPE A1107 15 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM GOL GLYCEROL HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN DTT 1,4-DITHIOTHREITOL HETSYN EPE HEPES FORMUL 2 MES 3(C6 H13 N O4 S) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 DTT C4 H10 O2 S2 FORMUL 8 EPE C8 H18 N2 O4 S FORMUL 9 HOH *214(H2 O) HELIX 1 AA1 ASP A 44 SER A 49 1 6 HELIX 2 AA2 LEU A 108 GLY A 118 1 11 HELIX 3 AA3 ASP A 128 GLN A 130 5 3 HELIX 4 AA4 ASP A 144 PHE A 149 1 6 HELIX 5 AA5 GLU A 206 LEU A 208 5 3 HELIX 6 AA6 THR A 209 GLY A 220 1 12 HELIX 7 AA7 SER A 226 MET A 230 5 5 HELIX 8 AA8 SER A 240 LEU A 254 1 15 HELIX 9 AA9 PHE A 267 THR A 280 1 14 HELIX 10 AB1 LEU A 331 GLU A 339 1 9 HELIX 11 AB2 LYS A 345 PHE A 354 1 10 HELIX 12 AB3 GLY A 380 THR A 390 1 11 HELIX 13 AB4 ASP A 439 ASP A 446 1 8 HELIX 14 AB5 ASN A 448 TYR A 473 1 26 HELIX 15 AB6 GLY A 474 VAL A 487 1 14 HELIX 16 AB7 ARG A 497 ILE A 502 1 6 HELIX 17 AB8 ILE A 502 THR A 513 1 12 HELIX 18 AB9 SER A 552 ASN A 562 1 11 HELIX 19 AC1 ASN A 576 TYR A 591 1 16 HELIX 20 AC2 GLY A 621 ALA A 644 1 24 HELIX 21 AC3 SER A 646 PHE A 673 1 28 HELIX 22 AC4 SER A 680 ASN A 703 1 24 HELIX 23 AC5 ASP A 763 ARG A 781 1 19 HELIX 24 AC6 SER A 836 GLU A 856 1 21 HELIX 25 AC7 SER A 861 ARG A 883 1 23 HELIX 26 AC8 PRO A 886 MET A 891 5 6 HELIX 27 AC9 ASN A 905 ASN A 918 1 14 HELIX 28 AD1 ASN A 946 THR A 949 5 4 HELIX 29 AD2 PHE A 967 LEU A 983 1 17 HELIX 30 AD3 LYS A 986 GLY A 998 1 13 SHEET 1 AA1 7 LEU A 132 LYS A 134 0 SHEET 2 AA1 7 CYS A 139 CYS A 142 -1 O HIS A 141 N THR A 133 SHEET 3 AA1 7 THR A 29 PRO A 35 1 N ARG A 33 O TYR A 140 SHEET 4 AA1 7 PHE A 17 CYS A 24 -1 N LEU A 18 O PHE A 34 SHEET 5 AA1 7 ASP A 2 GLU A 10 -1 N PHE A 9 O TYR A 19 SHEET 6 AA1 7 CYS A 124 SER A 126 -1 O TYR A 125 N VAL A 3 SHEET 7 AA1 7 LYS A 151 ILE A 153 -1 O ILE A 153 N CYS A 124 SHEET 1 AA2 4 PHE A 38 THR A 43 0 SHEET 2 AA2 4 CYS A 83 GLU A 93 -1 O TRP A 89 N VAL A 42 SHEET 3 AA2 4 ASN A 56 ASP A 67 -1 N LEU A 60 O MET A 88 SHEET 4 AA2 4 THR A 515 VAL A 518 1 O ILE A 516 N ARG A 64 SHEET 1 AA3 4 ILE A 72 SER A 73 0 SHEET 2 AA3 4 LEU A 568 SER A 574 1 O VAL A 571 N SER A 73 SHEET 3 AA3 4 SER A 610 ASP A 616 -1 O ILE A 612 N VAL A 572 SHEET 4 AA3 4 TYR A 596 HIS A 600 -1 N VAL A 599 O ALA A 613 SHEET 1 AA4 7 LEU A 222 ARG A 223 0 SHEET 2 AA4 7 LEU A 236 CYS A 239 1 O LEU A 238 N LEU A 222 SHEET 3 AA4 7 ARG A 197 ASN A 204 1 N ILE A 203 O VAL A 237 SHEET 4 AA4 7 ILE A 183 ILE A 191 -1 N THR A 186 O LEU A 202 SHEET 5 AA4 7 TYR A 162 CYS A 169 -1 N ALA A 166 O SER A 187 SHEET 6 AA4 7 TYR A 258 THR A 261 1 O TYR A 258 N LEU A 163 SHEET 7 AA4 7 ILE A 327 ASP A 330 1 O PHE A 329 N VAL A 259 SHEET 1 AA5 2 ILE A 285 ARG A 287 0 SHEET 2 AA5 2 ALA A 294 HIS A 296 -1 O VAL A 295 N PHE A 286 SHEET 1 AA6 2 TYR A 300 ASN A 303 0 SHEET 2 AA6 2 THR A 316 HIS A 319 -1 O HIS A 319 N TYR A 300 SHEET 1 AA7 7 SER A 355 ASN A 362 0 SHEET 2 AA7 7 MET A 368 GLY A 372 -1 O ILE A 371 N LYS A 359 SHEET 3 AA7 7 PHE A 415 LEU A 419 -1 O VAL A 417 N PHE A 370 SHEET 4 AA7 7 ILE A 401 ILE A 410 -1 N ASP A 409 O LYS A 416 SHEET 5 AA7 7 TYR A 394 VAL A 397 -1 N VAL A 397 O ILE A 401 SHEET 6 AA7 7 THR A 428 SER A 432 -1 O SER A 432 N THR A 396 SHEET 7 AA7 7 SER A 355 ASN A 362 -1 N GLY A 358 O TYR A 429 SHEET 1 AA8 9 ILE A 732 LYS A 734 0 SHEET 2 AA8 9 MET A 711 ARG A 713 -1 N LEU A 712 O VAL A 733 SHEET 3 AA8 9 GLU A 706 SER A 708 -1 N GLU A 706 O ARG A 713 SHEET 4 AA8 9 PHE A 743 GLY A 750 -1 O PHE A 743 N LEU A 707 SHEET 5 AA8 9 SER A 754 ILE A 759 -1 O PHE A 756 N TYR A 749 SHEET 6 AA8 9 VAL A 545 TYR A 550 -1 N LEU A 546 O THR A 757 SHEET 7 AA8 9 ILE A 789 MET A 800 -1 O TYR A 795 N VAL A 545 SHEET 8 AA8 9 TYR A 806 SER A 812 -1 O THR A 807 N ILE A 799 SHEET 9 AA8 9 GLU A 822 ASN A 825 -1 O GLU A 822 N LYS A 810 SHEET 1 AA9 3 LEU A 892 MET A 895 0 SHEET 2 AA9 3 ARG A 927 PRO A 935 -1 O PHE A 930 N LEU A 892 SHEET 3 AA9 3 GLU A 951 ILE A 953 -1 O THR A 952 N ALA A 931 SHEET 1 AB1 3 LEU A 892 MET A 895 0 SHEET 2 AB1 3 ARG A 927 PRO A 935 -1 O PHE A 930 N LEU A 892 SHEET 3 AB1 3 GLN A 964 ILE A 966 -1 O ARG A 965 N CYS A 934 CISPEP 1 PRO A 593 PRO A 594 0 -0.75 SITE 1 AC1 7 LYS A 21 ARG A 23 THR A 29 TYR A 190 SITE 2 AC1 7 THR A 255 PHE A 256 GLU A 581 SITE 1 AC2 4 ARG A 302 TYR A 496 ARG A 497 THR A 500 SITE 1 AC3 12 TYR A 300 HIS A 319 VAL A 320 PHE A 328 SITE 2 AC3 12 PHE A 329 ASP A 330 SER A 333 SER A 491 SITE 3 AC3 12 PHE A 494 GLU A 495 HOH A1226 HOH A1231 SITE 1 AC4 2 ASP A 157 ASN A 937 SITE 1 AC5 6 TYR A 114 GLY A 118 ILE A 119 SER A 484 SITE 2 AC5 6 VAL A 487 LYS A 508 SITE 1 AC6 2 LYS A 478 ASP A 654 SITE 1 AC7 8 MET A 207 LEU A 208 THR A 209 ASN A 709 SITE 2 AC7 8 MET A 711 ARG A 713 LYS A 734 ILE A 739 CRYST1 133.524 133.524 229.492 90.00 90.00 120.00 P 31 2 1 6 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 0.007489 0.004324 0.000000 0.00000 SCALE2 0.000000 0.008648 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004357 0.00000