HEADER HYDROLASE 23-AUG-23 8QAM TITLE VACCINIA VIRUS URACIL DNA GLYCOSIDASE MUTANT I197K-V200E-L204K COMPND MOL_ID: 1; COMPND 2 MOLECULE: URACIL-DNA GLYCOSYLASE; COMPND 3 CHAIN: B, C; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: FIRST RESIDUES GAMGS ARE CLONING ATRIFACTS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VACCINIA VIRUS COPENHAGEN; SOURCE 3 ORGANISM_TAXID: 10249; SOURCE 4 GENE: OPG116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 STAR KEYWDS DNA POLYMERASE PROCESSIVITY FACTOR, DNA BINDING, DNA POLYMERASE KEYWDS 2 BINDING, HYDROLASE-REPLICATION COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.TARBOURIECH,W.P.BURMEISTER REVDAT 2 05-JUN-24 8QAM 1 JRNL REVDAT 1 08-MAY-24 8QAM 0 JRNL AUTH W.P.BURMEISTER,L.BOUTIN,A.C.BALESTRA,H.GROGER, JRNL AUTH 2 A.BALLANDRAS-COLAS,S.HUTIN,C.KRAFT,C.GRIMM,B.BOTTCHER, JRNL AUTH 3 U.FISCHER,N.TARBOURIECH,F.ISENI JRNL TITL STRUCTURE AND FLEXIBILITY OF THE DNA POLYMERASE HOLOENZYME JRNL TITL 2 OF VACCINIA VIRUS. JRNL REF PLOS PATHOG. V. 20 11652 2024 JRNL REFN ESSN 1553-7374 JRNL PMID 38768256 JRNL DOI 10.1371/JOURNAL.PPAT.1011652 REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 113557 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) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 6094 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.32 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7804 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.4670 REMARK 3 BIN FREE R VALUE SET COUNT : 454 REMARK 3 BIN FREE R VALUE : 0.4760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3554 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 738 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.08000 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): 0.044 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.045 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.520 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4043 ; 0.017 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3767 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5541 ; 2.118 ; 1.648 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8853 ; 1.613 ; 1.581 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 520 ; 6.868 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 203 ;33.859 ;23.054 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 741 ;13.775 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;16.756 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 531 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4506 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 835 ; 0.001 ; 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): 1877 ; 3.586 ; 1.856 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1876 ; 3.587 ; 1.856 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2380 ; 4.280 ; 2.792 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2381 ; 4.279 ; 2.792 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2166 ; 5.779 ; 2.398 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2151 ; 5.768 ; 2.393 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3105 ; 6.467 ; 3.365 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4940 ; 7.256 ;25.689 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4745 ; 6.903 ;24.271 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7809 ; 5.264 ; 3.000 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 : 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 8QAM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292132931. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 119652 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.318 REMARK 200 RESOLUTION RANGE LOW (A) : 40.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 13.29 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.13400 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22 % PEG4000, 100 MM LISO4, 100 MM REMARK 280 HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 80.83400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 80.83400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.64050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 80.83400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 80.83400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.64050 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 80.83400 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 80.83400 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 19.64050 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 80.83400 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 80.83400 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 19.64050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 B -4 REMARK 465 ALA B -3 REMARK 465 MET B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 GLY C -4 REMARK 465 ALA C -3 REMARK 465 MET C -2 REMARK 465 GLY C -1 REMARK 465 SER C 0 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 NH2 ARG B 167 O HOH B 401 1.77 REMARK 500 OD2 ASP B 114 O HOH B 403 1.95 REMARK 500 OD1 ASP B 138 O HOH B 404 2.02 REMARK 500 O HOH C 1104 O HOH C 1130 2.03 REMARK 500 OD2 ASP B 162 O HOH B 405 2.04 REMARK 500 C2 GOL C 1001 O HOH C 1105 2.08 REMARK 500 O HOH B 610 O HOH B 719 2.10 REMARK 500 OE1 GLN C 55 O HOH C 1101 2.11 REMARK 500 O HOH C 1111 O HOH C 1394 2.11 REMARK 500 OE1 GLU C 91 O HOH C 1102 2.12 REMARK 500 O HOH B 495 O HOH B 735 2.13 REMARK 500 O HOH B 616 O HOH B 679 2.14 REMARK 500 O HOH C 1311 O HOH C 1394 2.15 REMARK 500 O HOH B 713 O HOH B 740 2.16 REMARK 500 O HOH C 1419 O HOH C 1427 2.17 REMARK 500 O HOH C 1435 O HOH C 1460 2.17 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 B 628 O HOH C 1122 7454 2.09 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 SER B 153 CA SER B 153 CB 0.101 REMARK 500 TYR B 218 N TYR B 218 CA 0.209 REMARK 500 TYR B 218 C TYR B 218 OXT 0.313 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 B 39 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG B 39 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG B 167 CB - CG - CD ANGL. DEV. = -23.0 DEGREES REMARK 500 ARG B 167 NE - CZ - NH1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG B 167 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 TYR B 218 N - CA - CB ANGL. DEV. = -14.6 DEGREES REMARK 500 TYR B 218 CA - C - O ANGL. DEV. = 15.5 DEGREES REMARK 500 PHE C 49 CB - CG - CD1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG C 58 CD - NE - CZ ANGL. DEV. = 10.9 DEGREES REMARK 500 ARG C 58 NE - CZ - NH1 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG C 58 NE - CZ - NH2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG C 61 NE - CZ - NH1 ANGL. DEV. = 4.9 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 TYR B 11 -38.00 76.88 REMARK 500 PHE B 79 -11.82 73.89 REMARK 500 PRO B 173 44.81 -90.36 REMARK 500 TYR C 11 -40.87 77.79 REMARK 500 TYR C 11 -39.45 77.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASN C 165 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 751 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH B 752 DISTANCE = 6.97 ANGSTROMS REMARK 525 HOH B 753 DISTANCE = 6.99 ANGSTROMS DBREF 8QAM B 1 218 UNP P20536 UNG_VACCC 1 218 DBREF 8QAM C 1 218 UNP P20536 UNG_VACCC 1 218 SEQADV 8QAM GLY B -4 UNP P20536 EXPRESSION TAG SEQADV 8QAM ALA B -3 UNP P20536 EXPRESSION TAG SEQADV 8QAM MET B -2 UNP P20536 EXPRESSION TAG SEQADV 8QAM GLY B -1 UNP P20536 EXPRESSION TAG SEQADV 8QAM SER B 0 UNP P20536 EXPRESSION TAG SEQADV 8QAM LYS B 197 UNP P20536 ILE 197 ENGINEERED MUTATION SEQADV 8QAM GLU B 200 UNP P20536 VAL 200 ENGINEERED MUTATION SEQADV 8QAM LYS B 204 UNP P20536 LEU 204 ENGINEERED MUTATION SEQADV 8QAM GLY C -4 UNP P20536 EXPRESSION TAG SEQADV 8QAM ALA C -3 UNP P20536 EXPRESSION TAG SEQADV 8QAM MET C -2 UNP P20536 EXPRESSION TAG SEQADV 8QAM GLY C -1 UNP P20536 EXPRESSION TAG SEQADV 8QAM SER C 0 UNP P20536 EXPRESSION TAG SEQADV 8QAM LYS C 197 UNP P20536 ILE 197 ENGINEERED MUTATION SEQADV 8QAM GLU C 200 UNP P20536 VAL 200 ENGINEERED MUTATION SEQADV 8QAM LYS C 204 UNP P20536 LEU 204 ENGINEERED MUTATION SEQRES 1 B 223 GLY ALA MET GLY SER MET ASN SER VAL THR VAL SER HIS SEQRES 2 B 223 ALA PRO TYR THR ILE THR TYR HIS ASP ASP TRP GLU PRO SEQRES 3 B 223 VAL MET SER GLN LEU VAL GLU PHE TYR ASN GLU VAL ALA SEQRES 4 B 223 SER TRP LEU LEU ARG ASP GLU THR SER PRO ILE PRO ASP SEQRES 5 B 223 LYS PHE PHE ILE GLN LEU LYS GLN PRO LEU ARG ASN LYS SEQRES 6 B 223 ARG VAL CYS VAL CYS GLY ILE ASP PRO TYR PRO LYS ASP SEQRES 7 B 223 GLY THR GLY VAL PRO PHE GLU SER PRO ASN PHE THR LYS SEQRES 8 B 223 LYS SER ILE LYS GLU ILE ALA SER SER ILE SER ARG LEU SEQRES 9 B 223 THR GLY VAL ILE ASP TYR LYS GLY TYR ASN LEU ASN ILE SEQRES 10 B 223 ILE ASP GLY VAL ILE PRO TRP ASN TYR TYR LEU SER CYS SEQRES 11 B 223 LYS LEU GLY GLU THR LYS SER HIS ALA ILE TYR TRP ASP SEQRES 12 B 223 LYS ILE SER LYS LEU LEU LEU GLN HIS ILE THR LYS HIS SEQRES 13 B 223 VAL SER VAL LEU TYR CYS LEU GLY LYS THR ASP PHE SER SEQRES 14 B 223 ASN ILE ARG ALA LYS LEU GLU SER PRO VAL THR THR ILE SEQRES 15 B 223 VAL GLY TYR HIS PRO ALA ALA ARG ASP ARG GLN PHE GLU SEQRES 16 B 223 LYS ASP ARG SER PHE GLU LYS ILE ASN GLU LEU LEU GLU SEQRES 17 B 223 LYS ASP ASN LYS VAL PRO ILE ASN TRP ALA GLN GLY PHE SEQRES 18 B 223 ILE TYR SEQRES 1 C 223 GLY ALA MET GLY SER MET ASN SER VAL THR VAL SER HIS SEQRES 2 C 223 ALA PRO TYR THR ILE THR TYR HIS ASP ASP TRP GLU PRO SEQRES 3 C 223 VAL MET SER GLN LEU VAL GLU PHE TYR ASN GLU VAL ALA SEQRES 4 C 223 SER TRP LEU LEU ARG ASP GLU THR SER PRO ILE PRO ASP SEQRES 5 C 223 LYS PHE PHE ILE GLN LEU LYS GLN PRO LEU ARG ASN LYS SEQRES 6 C 223 ARG VAL CYS VAL CYS GLY ILE ASP PRO TYR PRO LYS ASP SEQRES 7 C 223 GLY THR GLY VAL PRO PHE GLU SER PRO ASN PHE THR LYS SEQRES 8 C 223 LYS SER ILE LYS GLU ILE ALA SER SER ILE SER ARG LEU SEQRES 9 C 223 THR GLY VAL ILE ASP TYR LYS GLY TYR ASN LEU ASN ILE SEQRES 10 C 223 ILE ASP GLY VAL ILE PRO TRP ASN TYR TYR LEU SER CYS SEQRES 11 C 223 LYS LEU GLY GLU THR LYS SER HIS ALA ILE TYR TRP ASP SEQRES 12 C 223 LYS ILE SER LYS LEU LEU LEU GLN HIS ILE THR LYS HIS SEQRES 13 C 223 VAL SER VAL LEU TYR CYS LEU GLY LYS THR ASP PHE SER SEQRES 14 C 223 ASN ILE ARG ALA LYS LEU GLU SER PRO VAL THR THR ILE SEQRES 15 C 223 VAL GLY TYR HIS PRO ALA ALA ARG ASP ARG GLN PHE GLU SEQRES 16 C 223 LYS ASP ARG SER PHE GLU LYS ILE ASN GLU LEU LEU GLU SEQRES 17 C 223 LYS ASP ASN LYS VAL PRO ILE ASN TRP ALA GLN GLY PHE SEQRES 18 C 223 ILE TYR HET GOL B 301 6 HET GOL B 302 6 HET GOL B 303 6 HET SO4 B 304 5 HET SO4 B 305 5 HET GOL C1001 6 HET GOL C1002 6 HET GOL C1003 6 HET SO4 C1004 5 HET SO4 C1005 5 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 6(C3 H8 O3) FORMUL 6 SO4 4(O4 S 2-) FORMUL 13 HOH *738(H2 O) HELIX 1 AA1 HIS B 16 ASP B 18 5 3 HELIX 2 AA2 TRP B 19 LEU B 38 1 20 HELIX 3 AA3 ILE B 45 PHE B 49 5 5 HELIX 4 AA4 PHE B 50 GLN B 55 5 6 HELIX 5 AA5 LYS B 86 GLY B 101 1 16 HELIX 6 AA6 LEU B 110 ILE B 113 5 4 HELIX 7 AA7 HIS B 133 THR B 149 1 17 HELIX 8 AA8 GLY B 159 SER B 164 1 6 HELIX 9 AA9 ASN B 165 LEU B 170 5 6 HELIX 10 AB1 ARG B 193 ASP B 205 1 13 HELIX 11 AB2 ASN B 211 GLN B 214 5 4 HELIX 12 AB3 HIS C 16 PRO C 21 5 6 HELIX 13 AB4 VAL C 22 ARG C 39 1 18 HELIX 14 AB5 ILE C 45 PHE C 49 5 5 HELIX 15 AB6 PHE C 50 GLN C 55 5 6 HELIX 16 AB7 LYS C 86 GLY C 101 1 16 HELIX 17 AB8 LEU C 110 ILE C 113 5 4 HELIX 18 AB9 HIS C 133 VAL C 152 1 20 HELIX 19 AC1 GLY C 159 SER C 164 1 6 HELIX 20 AC2 ASN C 165 GLU C 171 1 7 HELIX 21 AC3 ARG C 187 ARG C 193 1 7 HELIX 22 AC4 ARG C 193 ASP C 205 1 13 HELIX 23 AC5 ASN C 211 GLN C 214 5 4 SHEET 1 AA1 2 ASN B 2 THR B 5 0 SHEET 2 AA1 2 THR B 12 TYR B 15 -1 O ILE B 13 N VAL B 4 SHEET 1 AA2 2 THR B 42 SER B 43 0 SHEET 2 AA2 2 CYS B 125 LYS B 126 -1 O CYS B 125 N SER B 43 SHEET 1 AA3 4 VAL B 116 ASN B 120 0 SHEET 2 AA3 4 VAL B 62 GLY B 66 1 N VAL B 64 O TRP B 119 SHEET 3 AA3 4 VAL B 154 LEU B 158 1 O TYR B 156 N CYS B 63 SHEET 4 AA3 4 THR B 175 GLY B 179 1 O ILE B 177 N CYS B 157 SHEET 1 AA4 2 GLY B 107 TYR B 108 0 SHEET 2 AA4 2 PHE B 216 ILE B 217 -1 O ILE B 217 N GLY B 107 SHEET 1 AA5 2 ASN C 2 THR C 5 0 SHEET 2 AA5 2 THR C 12 TYR C 15 -1 O ILE C 13 N VAL C 4 SHEET 1 AA6 2 THR C 42 SER C 43 0 SHEET 2 AA6 2 CYS C 125 LYS C 126 -1 O CYS C 125 N SER C 43 SHEET 1 AA7 4 VAL C 116 ASN C 120 0 SHEET 2 AA7 4 VAL C 62 GLY C 66 1 N VAL C 64 O TRP C 119 SHEET 3 AA7 4 VAL C 154 LEU C 158 1 O TYR C 156 N CYS C 63 SHEET 4 AA7 4 THR C 175 GLY C 179 1 O GLY C 179 N CYS C 157 SHEET 1 AA8 2 GLY C 107 TYR C 108 0 SHEET 2 AA8 2 PHE C 216 ILE C 217 -1 O ILE C 217 N GLY C 107 CISPEP 1 ALA B 9 PRO B 10 0 10.30 CISPEP 2 SER B 43 PRO B 44 0 -12.64 CISPEP 3 ALA C 9 PRO C 10 0 9.15 CISPEP 4 SER C 43 PRO C 44 0 -13.72 CRYST1 161.668 161.668 39.281 90.00 90.00 90.00 I 4 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 0.006186 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006186 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025458 0.00000