PDB Short entry for 5HRK HEADER TRANSFERASE/DNA 23-JAN-16 5HRK TITLE THE CRYSTAL STRUCTURE OF ASFVPOLX(H115F MUTANT): 1NT-GAP(P) DNA2:DGTP TITLE 2 TERNARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA-LIKE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PO174L, POLX; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3'); COMPND 9 CHAIN: F, C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'- COMPND 13 D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3'); COMPND 14 CHAIN: H, E; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3'); COMPND 18 CHAIN: G, D; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AFRICAN SWINE FEVER VIRUS; SOURCE 3 ORGANISM_COMMON: ASFV; SOURCE 4 ORGANISM_TAXID: 10497; SOURCE 5 GENE: O174L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 MOL_ID: 4; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630 KEYWDS ASFV, POLX, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.Q.CHEN,J.ZHANG,J.H.GAN REVDAT 2 08-NOV-23 5HRK 1 LINK REVDAT 1 18-JAN-17 5HRK 0 JRNL AUTH Y.Q.CHEN,J.ZHANG,J.H.GAN JRNL TITL THE CRYSTAL STRUCTURE OF SE-ASFVPOLX(L52/163M MUTANT) IN JRNL TITL 2 COMPLEX WITH 1NT-GAP DNA1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 16476 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 840 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.0281 - 5.2523 0.99 2670 164 0.1851 0.2143 REMARK 3 2 5.2523 - 4.1733 1.00 2668 131 0.2247 0.2599 REMARK 3 3 4.1733 - 3.6471 0.99 2612 131 0.2580 0.3307 REMARK 3 4 3.6471 - 3.3142 0.97 2569 154 0.2648 0.3121 REMARK 3 5 3.3142 - 3.0770 0.96 2567 124 0.3096 0.3760 REMARK 3 6 3.0770 - 2.8957 0.96 2550 136 0.3425 0.3968 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 4381 REMARK 3 ANGLE : 1.540 6262 REMARK 3 CHIRALITY : 0.089 728 REMARK 3 PLANARITY : 0.011 533 REMARK 3 DIHEDRAL : 23.365 2328 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A):-158.7750-104.2499-180.1197 REMARK 3 T TENSOR REMARK 3 T11: 0.4893 T22: 0.3861 REMARK 3 T33: 0.5982 T12: -0.0136 REMARK 3 T13: -0.1006 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 1.4050 L22: 0.6324 REMARK 3 L33: 3.7218 L12: 0.0783 REMARK 3 L13: 0.3712 L23: 0.5239 REMARK 3 S TENSOR REMARK 3 S11: 0.1041 S12: 0.1556 S13: -0.1380 REMARK 3 S21: 0.0088 S22: 0.0512 S23: -0.0093 REMARK 3 S31: 0.0954 S32: -0.1505 S33: -0.1238 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5HRK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000217609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16476 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: 2HR9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 3350 200 MM SODIUM REMARK 280 IODIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z 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 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 1.000000 0.000000 0.000000 53.36300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.59800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.36300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.59800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F, H, G 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, E, D 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 SER A -3 REMARK 465 GLY A -2 REMARK 465 GLY A -1 REMARK 465 GLY A 0 REMARK 465 SER B -3 REMARK 465 GLY B -2 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 MET A 1 CG SD CE REMARK 470 LEU A 2 CG CD1 CD2 REMARK 470 ILE A 5 CG1 CG2 CD1 REMARK 470 GLN A 6 CG CD OE1 NE2 REMARK 470 LYS A 8 CG CD CE NZ REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 ARG A 17 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 GLN A 25 CG CD OE1 NE2 REMARK 470 ILE A 27 CG1 CG2 CD1 REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 ILE A 29 CG1 CG2 CD1 REMARK 470 LYS A 32 CG CD CE NZ REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 LYS A 63 CG CD CE NZ REMARK 470 LYS A 72 CG CD CE NZ REMARK 470 VAL A 87 CG1 CG2 REMARK 470 GLU A 93 CG CD OE1 OE2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 LYS A 95 CG CD CE NZ REMARK 470 GLU A 107 CG CD OE1 OE2 REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 LYS A 132 CG CD CE NZ REMARK 470 LYS A 136 CG CD CE NZ REMARK 470 PHE A 143 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 144 CG CD CE NZ REMARK 470 ASN A 145 CG OD1 ND2 REMARK 470 GLN A 146 CG CD OE1 NE2 REMARK 470 LYS A 152 CG CD CE NZ REMARK 470 LEU A 163 CG CD1 CD2 REMARK 470 LYS B 8 CG CD CE NZ REMARK 470 LYS B 9 CG CD CE NZ REMARK 470 GLN B 25 CG CD OE1 NE2 REMARK 470 LYS B 28 CG CD CE NZ REMARK 470 LYS B 32 CG CD CE NZ REMARK 470 LYS B 45 CG CD CE NZ REMARK 470 GLU B 58 CG CD OE1 OE2 REMARK 470 LYS B 59 CG CD CE NZ REMARK 470 LYS B 60 CG CD CE NZ REMARK 470 LYS B 63 CG CD CE NZ REMARK 470 LYS B 72 CG CD CE NZ REMARK 470 THR B 96 OG1 CG2 REMARK 470 LYS B 131 CG CD CE NZ REMARK 470 LYS B 132 CG CD CE NZ REMARK 470 LYS B 133 CG CD CE NZ REMARK 470 LYS B 136 CG CD CE NZ REMARK 470 LYS B 144 CG CD CE NZ REMARK 470 ASN B 145 CG OD1 ND2 REMARK 470 GLN B 146 CG CD OE1 NE2 REMARK 470 LEU B 148 CG CD1 CD2 REMARK 470 LYS B 152 CG CD CE NZ REMARK 470 LYS B 157 CG CD CE NZ REMARK 470 LYS B 161 CG CD CE NZ REMARK 470 PHE B 165 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 171 CG CD CE NZ REMARK 470 LYS B 172 CG CD CE NZ REMARK 470 DA F 9 O3' REMARK 470 DA C 9 O3' 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 A 125 C LEU A 174 1.72 REMARK 500 NH2 ARG A 125 OXT LEU A 174 1.73 REMARK 500 OG SER A 39 O3B DGT A 201 2.06 REMARK 500 OH TYR A 140 OP1 DT H 12 2.15 REMARK 500 N2 DG F 1 O2 DC H 18 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 111 CG TYR A 111 CD2 -0.106 REMARK 500 TYR A 111 CE1 TYR A 111 CZ -0.081 REMARK 500 TYR A 111 CZ TYR A 111 CE2 -0.100 REMARK 500 DA G 1 P DA G 1 OP3 -0.126 REMARK 500 DG E 9 O3' DG E 9 C3' -0.067 REMARK 500 DA D 1 P DA D 1 OP3 -0.120 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 LEU A 74 CB - CG - CD1 ANGL. DEV. = -12.6 DEGREES REMARK 500 VAL A 80 CG1 - CB - CG2 ANGL. DEV. = -9.7 DEGREES REMARK 500 LEU B 14 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 LEU B 26 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 DT F 2 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG F 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC H 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT H 8 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT H 15 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT C 2 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC C 8 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT E 8 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC E 18 O4' - C1' - N1 ANGL. DEV. = 2.6 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 ALA A 19 161.07 179.70 REMARK 500 LYS A 32 -1.93 -59.06 REMARK 500 ASN A 68 45.39 -108.81 REMARK 500 GLU A 93 -129.23 57.14 REMARK 500 GLN A 146 3.99 83.08 REMARK 500 LYS B 32 -3.73 -58.85 REMARK 500 SER B 39 -39.05 -35.23 REMARK 500 LYS B 109 -70.59 -43.79 REMARK 500 THR B 154 -49.48 -131.12 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 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 49 OD1 REMARK 620 2 ASP A 51 OD2 97.5 REMARK 620 3 DGT A 201 O3G 77.9 167.1 REMARK 620 4 DGT A 201 O2B 167.1 81.2 100.5 REMARK 620 5 DGT A 201 O2A 77.4 76.7 90.5 89.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 49 OD2 REMARK 620 2 ASP A 51 OD1 78.7 REMARK 620 3 ASP A 100 OD2 69.6 82.9 REMARK 620 4 DGT A 201 O2A 90.8 94.0 160.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 49 OD1 REMARK 620 2 ASP B 51 OD2 114.1 REMARK 620 3 DGT B 201 O3G 66.9 170.9 REMARK 620 4 DGT B 201 O2B 147.4 91.8 90.7 REMARK 620 5 DGT B 201 O2A 75.8 83.1 105.8 88.9 REMARK 620 6 HOH B 301 O 121.2 57.7 113.6 88.8 140.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 49 OD2 REMARK 620 2 ASP B 51 OD1 59.9 REMARK 620 3 ASP B 100 OD2 90.3 74.2 REMARK 620 4 DGT B 201 O2A 79.1 82.7 156.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DGT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DGT B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5HR9 RELATED DB: PDB REMARK 900 RELATED ID: 5HRB RELATED DB: PDB REMARK 900 RELATED ID: 5HRD RELATED DB: PDB REMARK 900 RELATED ID: 5HRE RELATED DB: PDB REMARK 900 RELATED ID: 5HRF RELATED DB: PDB REMARK 900 RELATED ID: 5HRG RELATED DB: PDB REMARK 900 RELATED ID: 5HRH RELATED DB: PDB REMARK 900 RELATED ID: 5HRK RELATED DB: PDB REMARK 900 RELATED ID: 5HRL RELATED DB: PDB DBREF1 5HRK A 1 174 UNP A0A0A1E3N6_ASF DBREF2 5HRK A A0A0A1E3N6 1 174 DBREF1 5HRK B 1 174 UNP A0A0A1E3N6_ASF DBREF2 5HRK B A0A0A1E3N6 1 174 DBREF 5HRK F 1 9 PDB 5HRK 5HRK 1 9 DBREF 5HRK H 1 18 PDB 5HRK 5HRK 1 18 DBREF 5HRK G 1 8 PDB 5HRK 5HRK 1 8 DBREF 5HRK C 1 9 PDB 5HRK 5HRK 1 9 DBREF 5HRK E 1 18 PDB 5HRK 5HRK 1 18 DBREF 5HRK D 1 8 PDB 5HRK 5HRK 1 8 SEQADV 5HRK SER A -3 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRK GLY A -2 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRK GLY A -1 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRK GLY A 0 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRK PHE A 115 UNP A0A0A1E3N HIS 115 ENGINEERED MUTATION SEQADV 5HRK SER B -3 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRK GLY B -2 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRK GLY B -1 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRK GLY B 0 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRK PHE B 115 UNP A0A0A1E3N HIS 115 ENGINEERED MUTATION SEQRES 1 A 178 SER GLY GLY GLY MET LEU THR LEU ILE GLN GLY LYS LYS SEQRES 2 A 178 ILE VAL ASN HIS LEU ARG SER ARG LEU ALA PHE GLU TYR SEQRES 3 A 178 ASN GLY GLN LEU ILE LYS ILE LEU SER LYS ASN ILE VAL SEQRES 4 A 178 ALA VAL GLY SER LEU ARG ARG GLU GLU LYS MET LEU ASN SEQRES 5 A 178 ASP VAL ASP LEU LEU ILE ILE VAL PRO GLU LYS LYS LEU SEQRES 6 A 178 LEU LYS HIS VAL LEU PRO ASN ILE ARG ILE LYS GLY LEU SEQRES 7 A 178 SER PHE SER VAL LYS VAL CYS GLY GLU ARG LYS CYS VAL SEQRES 8 A 178 LEU PHE ILE GLU TRP GLU LYS LYS THR TYR GLN LEU ASP SEQRES 9 A 178 LEU PHE THR ALA LEU ALA GLU GLU LYS PRO TYR ALA ILE SEQRES 10 A 178 PHE PHE PHE THR GLY PRO VAL SER TYR LEU ILE ARG ILE SEQRES 11 A 178 ARG ALA ALA LEU LYS LYS LYS ASN TYR LYS LEU ASN GLN SEQRES 12 A 178 TYR GLY LEU PHE LYS ASN GLN THR LEU VAL PRO LEU LYS SEQRES 13 A 178 ILE THR THR GLU LYS GLU LEU ILE LYS GLU LEU GLY PHE SEQRES 14 A 178 THR TYR ARG ILE PRO LYS LYS ARG LEU SEQRES 1 B 178 SER GLY GLY GLY MET LEU THR LEU ILE GLN GLY LYS LYS SEQRES 2 B 178 ILE VAL ASN HIS LEU ARG SER ARG LEU ALA PHE GLU TYR SEQRES 3 B 178 ASN GLY GLN LEU ILE LYS ILE LEU SER LYS ASN ILE VAL SEQRES 4 B 178 ALA VAL GLY SER LEU ARG ARG GLU GLU LYS MET LEU ASN SEQRES 5 B 178 ASP VAL ASP LEU LEU ILE ILE VAL PRO GLU LYS LYS LEU SEQRES 6 B 178 LEU LYS HIS VAL LEU PRO ASN ILE ARG ILE LYS GLY LEU SEQRES 7 B 178 SER PHE SER VAL LYS VAL CYS GLY GLU ARG LYS CYS VAL SEQRES 8 B 178 LEU PHE ILE GLU TRP GLU LYS LYS THR TYR GLN LEU ASP SEQRES 9 B 178 LEU PHE THR ALA LEU ALA GLU GLU LYS PRO TYR ALA ILE SEQRES 10 B 178 PHE PHE PHE THR GLY PRO VAL SER TYR LEU ILE ARG ILE SEQRES 11 B 178 ARG ALA ALA LEU LYS LYS LYS ASN TYR LYS LEU ASN GLN SEQRES 12 B 178 TYR GLY LEU PHE LYS ASN GLN THR LEU VAL PRO LEU LYS SEQRES 13 B 178 ILE THR THR GLU LYS GLU LEU ILE LYS GLU LEU GLY PHE SEQRES 14 B 178 THR TYR ARG ILE PRO LYS LYS ARG LEU SEQRES 1 F 9 DG DT DG DA DG DT DA DC DA SEQRES 1 H 18 DC DG DT DT DC DT DA DT DG DT DG DT DA SEQRES 2 H 18 DC DT DC DA DC SEQRES 1 G 8 DA DT DA DG DA DA DC DG SEQRES 1 C 9 DG DT DG DA DG DT DA DC DA SEQRES 1 E 18 DC DG DT DT DC DT DA DT DG DT DG DT DA SEQRES 2 E 18 DC DT DC DA DC SEQRES 1 D 8 DA DT DA DG DA DA DC DG HET DGT A 201 31 HET MN A 202 1 HET MN A 203 1 HET SO4 A 204 5 HET SO4 A 205 5 HET DGT B 201 31 HET MN B 202 1 HET MN B 203 1 HET SO4 B 204 5 HET SO4 B 205 5 HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION FORMUL 9 DGT 2(C10 H16 N5 O13 P3) FORMUL 10 MN 4(MN 2+) FORMUL 12 SO4 4(O4 S 2-) FORMUL 19 HOH *2(H2 O) HELIX 1 AA1 LEU A 4 ARG A 15 1 12 HELIX 2 AA2 LEU A 30 LYS A 32 5 3 HELIX 3 AA3 GLY A 38 ARG A 41 5 4 HELIX 4 AA4 GLU A 58 LEU A 62 5 5 HELIX 5 AA5 GLU A 108 GLY A 118 1 11 HELIX 6 AA6 PRO A 119 LYS A 133 1 15 HELIX 7 AA7 THR A 155 GLY A 164 1 10 HELIX 8 AA8 ILE A 169 ARG A 173 5 5 HELIX 9 AA9 LEU B 4 ARG B 15 1 12 HELIX 10 AB1 LEU B 30 LYS B 32 5 3 HELIX 11 AB2 GLY B 38 ARG B 41 5 4 HELIX 12 AB3 GLU B 58 LYS B 60 5 3 HELIX 13 AB4 LEU B 61 LEU B 66 1 6 HELIX 14 AB5 GLU B 108 GLY B 118 1 11 HELIX 15 AB6 PRO B 119 LYS B 133 1 15 HELIX 16 AB7 THR B 155 GLY B 164 1 10 SHEET 1 AA1 2 LEU A 2 THR A 3 0 SHEET 2 AA1 2 MET A 46 LEU A 47 -1 O LEU A 47 N LEU A 2 SHEET 1 AA2 3 LEU A 26 LYS A 28 0 SHEET 2 AA2 3 LEU A 18 GLU A 21 -1 N PHE A 20 O ILE A 27 SHEET 3 AA2 3 ILE A 69 ILE A 71 -1 O ARG A 70 N ALA A 19 SHEET 1 AA3 5 ILE A 34 VAL A 37 0 SHEET 2 AA3 5 VAL A 50 VAL A 56 -1 O ASP A 51 N VAL A 37 SHEET 3 AA3 5 LYS A 95 LEU A 105 1 O PHE A 102 N ILE A 54 SHEET 4 AA3 5 LYS A 85 TRP A 92 -1 N LEU A 88 O LEU A 99 SHEET 5 AA3 5 PHE A 76 VAL A 80 -1 N SER A 77 O PHE A 89 SHEET 1 AA4 3 LYS A 136 LEU A 137 0 SHEET 2 AA4 3 LEU A 142 LYS A 144 -1 O PHE A 143 N LYS A 136 SHEET 3 AA4 3 THR A 147 LEU A 148 -1 O THR A 147 N LYS A 144 SHEET 1 AA5 2 LEU B 2 THR B 3 0 SHEET 2 AA5 2 MET B 46 LEU B 47 -1 O LEU B 47 N LEU B 2 SHEET 1 AA6 3 LEU B 26 LYS B 28 0 SHEET 2 AA6 3 LEU B 18 GLU B 21 -1 N PHE B 20 O ILE B 27 SHEET 3 AA6 3 ILE B 69 ILE B 71 -1 O ARG B 70 N ALA B 19 SHEET 1 AA7 4 ILE B 34 VAL B 37 0 SHEET 2 AA7 4 ASP B 49 VAL B 56 -1 O ASP B 51 N VAL B 37 SHEET 3 AA7 4 LYS B 95 LEU B 105 1 O ALA B 104 N ILE B 54 SHEET 4 AA7 4 LEU B 88 TRP B 92 -1 N LEU B 88 O LEU B 99 SHEET 1 AA8 3 LYS B 136 LEU B 137 0 SHEET 2 AA8 3 LEU B 142 LYS B 144 -1 O PHE B 143 N LYS B 136 SHEET 3 AA8 3 THR B 147 LEU B 148 -1 O THR B 147 N LYS B 144 SSBOND 1 CYS A 81 CYS A 86 1555 1555 2.08 SSBOND 2 CYS B 81 CYS B 86 1555 1555 2.04 LINK NH2 ARG A 125 O LEU A 174 1555 1555 1.41 LINK OD1 ASP A 49 MN MN A 202 1555 1555 2.01 LINK OD2 ASP A 49 MN MN A 203 1555 1555 2.52 LINK OD2 ASP A 51 MN MN A 202 1555 1555 1.79 LINK OD1 ASP A 51 MN MN A 203 1555 1555 2.06 LINK OD2 ASP A 100 MN MN A 203 1555 1555 2.05 LINK O3G DGT A 201 MN MN A 202 1555 1555 2.20 LINK O2B DGT A 201 MN MN A 202 1555 1555 2.39 LINK O2A DGT A 201 MN MN A 202 1555 1555 2.36 LINK O2A DGT A 201 MN MN A 203 1555 1555 1.75 LINK OD1 ASP B 49 MN MN B 202 1555 1555 2.68 LINK OD2 ASP B 49 MN MN B 203 1555 1555 2.65 LINK OD2 ASP B 51 MN MN B 202 1555 1555 1.98 LINK OD1 ASP B 51 MN MN B 203 1555 1555 2.59 LINK OD2 ASP B 100 MN MN B 203 1555 1555 1.83 LINK O3G DGT B 201 MN MN B 202 1555 1555 1.97 LINK O2B DGT B 201 MN MN B 202 1555 1555 2.39 LINK O2A DGT B 201 MN MN B 202 1555 1555 1.77 LINK O2A DGT B 201 MN MN B 203 1555 1555 2.35 LINK MN MN B 202 O HOH B 301 1555 1555 2.69 CISPEP 1 GLY A 118 PRO A 119 0 2.39 CISPEP 2 GLY B 118 PRO B 119 0 0.63 SITE 1 AC1 15 GLY A 38 SER A 39 ARG A 42 ASN A 48 SITE 2 AC1 15 ASP A 49 ASP A 51 PHE A 115 PHE A 116 SITE 3 AC1 15 THR A 117 GLY A 118 VAL A 120 MN A 202 SITE 4 AC1 15 MN A 203 DA F 9 DG H 9 SITE 1 AC2 5 ASP A 49 ASP A 51 DGT A 201 MN A 203 SITE 2 AC2 5 HOH A 301 SITE 1 AC3 5 ASP A 49 ASP A 51 ASP A 100 DGT A 201 SITE 2 AC3 5 MN A 202 SITE 1 AC4 6 LYS A 109 PRO A 110 ILE A 113 THR A 154 SITE 2 AC4 6 THR A 155 GLU A 156 SITE 1 AC5 4 LYS A 136 PHE A 143 ASN A 145 GLN A 146 SITE 1 AC6 14 GLY B 38 SER B 39 ARG B 42 ASN B 48 SITE 2 AC6 14 ASP B 49 ASP B 51 PHE B 116 THR B 117 SITE 3 AC6 14 GLY B 118 VAL B 120 MN B 202 MN B 203 SITE 4 AC6 14 DA C 9 DG E 9 SITE 1 AC7 6 SER B 39 ASP B 49 ASP B 51 DGT B 201 SITE 2 AC7 6 MN B 203 HOH B 301 SITE 1 AC8 6 ASP B 49 ASP B 51 ASP B 100 DGT B 201 SITE 2 AC8 6 MN B 202 DA C 9 SITE 1 AC9 6 LYS B 109 PRO B 110 ILE B 113 THR B 154 SITE 2 AC9 6 THR B 155 GLU B 156 SITE 1 AD1 3 PHE B 143 GLN B 146 THR B 147 CRYST1 106.726 87.196 82.616 90.00 97.59 90.00 C 1 2 1 8 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 0.009370 0.000000 0.001249 0.00000 SCALE2 0.000000 0.011468 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012211 0.00000