HEADER TRANSFERASE/DNA 23-JAN-16 5HRL TITLE THE CRYSTAL STRUCTURE OF ASFVPOLX: 1NT-GAP(P) DNA2: DGTP TERNARY TITLE 2 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 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*CP*GP*TP*TP*CP*TP*AP*TP*GP*TP*GP*TP*AP*CP*TP*CP*AP*C)-3'); COMPND 9 CHAIN: C, F; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*TP*GP*AP*GP*TP*AP*CP*A)-3'); COMPND 13 CHAIN: D, G; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(P*AP*TP*AP*GP*AP*AP*CP*G)-3'); COMPND 17 CHAIN: E, H; COMPND 18 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: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 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 5HRL 1 LINK REVDAT 1 18-JAN-17 5HRL 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. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 28026 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1482 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1923 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.3900 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.4670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2811 REMARK 3 NUCLEIC ACID ATOMS : 1426 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.69000 REMARK 3 B22 (A**2) : 5.45000 REMARK 3 B33 (A**2) : 0.24000 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): 0.362 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.252 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.218 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.980 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4548 ; 0.008 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): 3753 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6423 ; 1.403 ; 1.698 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8653 ; 1.280 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 349 ; 5.368 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;35.836 ;23.036 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 553 ;15.201 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.208 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 671 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3969 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 985 ; 0.003 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 2 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 0 173 B 0 173 11077 0.06 0.05 REMARK 3 2 C 1 18 F 1 18 1510 0.01 0.05 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 5HRL 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_1000217610. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 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-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28026 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 95.2 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 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 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: 5HR9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 17% W/V PEG REMARK 280 10000, 0.1 M AMMONIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -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 62.32550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.67400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 62.32550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.67400 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: 5120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D, E 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: 14060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F, G, H 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 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 LYS A 9 NZ REMARK 470 LYS A 28 CD CE NZ REMARK 470 LYS A 32 NZ REMARK 470 LYS A 45 CE NZ REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 LYS A 59 CD CE NZ REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 LYS A 63 NZ REMARK 470 LYS A 72 CG CD CE NZ REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 LYS A 95 CD CE NZ REMARK 470 LYS A 144 CG CD CE NZ REMARK 470 LYS A 152 CG CD CE NZ REMARK 470 DA D 9 O3' REMARK 470 LYS B 9 CD CE NZ REMARK 470 ILE B 10 CD1 REMARK 470 LYS B 45 NZ REMARK 470 LYS B 59 NZ REMARK 470 LYS B 60 CG CD CE NZ REMARK 470 LYS B 72 CG CD CE NZ REMARK 470 LYS B 94 CG CD CE NZ REMARK 470 LYS B 95 CE NZ REMARK 470 GLU B 107 CG CD OE1 OE2 REMARK 470 LYS B 132 NZ REMARK 470 LYS B 152 CG CD CE NZ REMARK 470 LYS B 161 NZ REMARK 470 LYS B 171 NZ REMARK 470 DA G 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 O TYR B 135 O HOH B 301 2.13 REMARK 500 OE2 GLU A 44 O1 GOL A 204 2.19 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 DA E 1 P DA E 1 OP3 -0.129 REMARK 500 DA H 1 P DA H 1 OP3 -0.123 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 DC C 1 C5' - C4' - O4' ANGL. DEV. = 8.9 DEGREES REMARK 500 DC F 1 C5' - C4' - C3' ANGL. DEV. = 7.5 DEGREES REMARK 500 DC F 1 C5' - C4' - O4' ANGL. DEV. = 9.1 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 VAL A 65 -72.31 -56.78 REMARK 500 VAL B 37 -163.82 -129.18 REMARK 500 VAL B 65 -73.20 -56.22 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 80.5 REMARK 620 3 DGT A 201 O2G 104.7 171.7 REMARK 620 4 DGT A 201 O2B 168.0 90.8 83.1 REMARK 620 5 DGT A 201 O2A 98.4 96.4 89.2 90.8 REMARK 620 6 HOH A 301 O 85.4 80.5 93.3 85.1 174.8 REMARK 620 N 1 2 3 4 5 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 51 OD1 REMARK 620 2 ASP A 100 OD2 81.4 REMARK 620 3 DGT A 201 O2A 106.9 146.5 REMARK 620 N 1 2 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 83.6 REMARK 620 3 DGT B 201 O1G 101.5 173.7 REMARK 620 4 DGT B 201 O1B 170.7 89.7 84.8 REMARK 620 5 DGT B 201 O1A 98.5 93.9 89.0 88.4 REMARK 620 6 HOH B 305 O 82.5 81.2 95.8 90.1 174.8 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 51 OD1 REMARK 620 2 ASP B 100 OD2 81.1 REMARK 620 3 DGT B 201 O1A 106.9 149.0 REMARK 620 N 1 2 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 GOL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DGT B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 203 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: 5HRI RELATED DB: PDB REMARK 900 RELATED ID: 5HRK RELATED DB: PDB DBREF1 5HRL A 1 174 UNP A0A0A1E3N6_ASF DBREF2 5HRL A A0A0A1E3N6 1 174 DBREF 5HRL C 1 18 PDB 5HRL 5HRL 1 18 DBREF 5HRL D 1 9 PDB 5HRL 5HRL 1 9 DBREF 5HRL E 1 8 PDB 5HRL 5HRL 1 8 DBREF1 5HRL B 1 174 UNP A0A0A1E3N6_ASF DBREF2 5HRL B A0A0A1E3N6 1 174 DBREF 5HRL F 1 18 PDB 5HRL 5HRL 1 18 DBREF 5HRL G 1 9 PDB 5HRL 5HRL 1 9 DBREF 5HRL H 1 8 PDB 5HRL 5HRL 1 8 SEQADV 5HRL SER A -3 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRL GLY A -2 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRL GLY A -1 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRL GLY A 0 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRL SER B -3 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRL GLY B -2 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRL GLY B -1 UNP A0A0A1E3N EXPRESSION TAG SEQADV 5HRL GLY B 0 UNP A0A0A1E3N EXPRESSION TAG 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 HIS 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 C 18 DC DG DT DT DC DT DA DT DG DT DG DT DA SEQRES 2 C 18 DC DT DC DA DC SEQRES 1 D 9 DG DT DG DA DG DT DA DC DA SEQRES 1 E 8 DA DT DA DG DA DA DC DG 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 HIS 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 18 DC DG DT DT DC DT DA DT DG DT DG DT DA SEQRES 2 F 18 DC DT DC DA DC SEQRES 1 G 9 DG DT DG DA DG DT DA DC DA SEQRES 1 H 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 GOL A 204 6 HET DGT B 201 31 HET MN B 202 1 HET MN B 203 1 HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 9 DGT 2(C10 H16 N5 O13 P3) FORMUL 10 MN 4(MN 2+) FORMUL 12 GOL C3 H8 O3 FORMUL 16 HOH *45(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 VAL A 37 ARG A 42 1 6 HELIX 4 AA4 GLU A 58 HIS A 64 5 7 HELIX 5 AA5 VAL A 65 PRO A 67 5 3 HELIX 6 AA6 GLU A 108 GLY A 118 1 11 HELIX 7 AA7 PRO A 119 LYS A 133 1 15 HELIX 8 AA8 THR A 155 GLY A 164 1 10 HELIX 9 AA9 ILE A 169 ARG A 173 5 5 HELIX 10 AB1 LEU B 4 ARG B 15 1 12 HELIX 11 AB2 LEU B 30 LYS B 32 5 3 HELIX 12 AB3 VAL B 37 ARG B 42 1 6 HELIX 13 AB4 GLU B 58 HIS B 64 5 7 HELIX 14 AB5 VAL B 65 PRO B 67 5 3 HELIX 15 AB6 GLU B 108 GLY B 118 1 11 HELIX 16 AB7 PRO B 119 LYS B 133 1 15 HELIX 17 AB8 THR B 155 GLY B 164 1 10 HELIX 18 AB9 ILE B 169 ARG B 173 5 5 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 GLN A 25 LYS A 28 0 SHEET 2 AA2 3 LEU A 18 TYR A 22 -1 N TYR A 22 O GLN A 25 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 ALA A 36 0 SHEET 2 AA3 5 VAL A 50 VAL A 56 -1 O LEU A 53 N VAL A 35 SHEET 3 AA3 5 THR A 96 LEU A 105 1 O ASP A 100 N VAL A 50 SHEET 4 AA3 5 LYS A 85 GLU A 91 -1 N LEU A 88 O LEU A 99 SHEET 5 AA3 5 PHE A 76 CYS A 81 -1 N LYS A 79 O VAL A 87 SHEET 1 AA4 3 TYR A 135 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 GLN B 25 LYS B 28 0 SHEET 2 AA6 3 LEU B 18 TYR B 22 -1 N TYR B 22 O GLN B 25 SHEET 3 AA6 3 ILE B 69 ILE B 71 -1 O ARG B 70 N ALA B 19 SHEET 1 AA7 5 ILE B 34 ALA B 36 0 SHEET 2 AA7 5 VAL B 50 VAL B 56 -1 O LEU B 53 N VAL B 35 SHEET 3 AA7 5 THR B 96 LEU B 105 1 O ASP B 100 N VAL B 50 SHEET 4 AA7 5 LYS B 85 GLU B 91 -1 N CYS B 86 O LEU B 101 SHEET 5 AA7 5 PHE B 76 CYS B 81 -1 N VAL B 80 O VAL B 87 SHEET 1 AA8 3 TYR B 135 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 LINK OD1 ASP A 49 MN MN A 202 1555 1555 2.01 LINK OD2 ASP A 51 MN MN A 202 1555 1555 2.07 LINK OD1 ASP A 51 MN MN A 203 1555 1555 2.00 LINK OD2 ASP A 100 MN MN A 203 1555 1555 2.01 LINK O2G DGT A 201 MN MN A 202 1555 1555 2.05 LINK O2B DGT A 201 MN MN A 202 1555 1555 2.03 LINK O2A DGT A 201 MN MN A 202 1555 1555 2.04 LINK O2A DGT A 201 MN MN A 203 1555 1555 2.04 LINK MN MN A 202 O HOH A 301 1555 1555 2.03 LINK OD1 ASP B 49 MN MN B 202 1555 1555 2.01 LINK OD2 ASP B 51 MN MN B 202 1555 1555 2.07 LINK OD1 ASP B 51 MN MN B 203 1555 1555 2.02 LINK OD2 ASP B 100 MN MN B 203 1555 1555 2.09 LINK O1G DGT B 201 MN MN B 202 1555 1555 2.06 LINK O1B DGT B 201 MN MN B 202 1555 1555 2.02 LINK O1A DGT B 201 MN MN B 202 1555 1555 2.04 LINK O1A DGT B 201 MN MN B 203 1555 1555 1.98 LINK MN MN B 202 O HOH B 305 1555 1555 2.05 CISPEP 1 GLY A 118 PRO A 119 0 -3.75 CISPEP 2 GLY B 118 PRO B 119 0 -4.68 SITE 1 AC1 22 GLY A 38 SER A 39 ARG A 42 ASN A 48 SITE 2 AC1 22 ASP A 49 ASP A 51 HIS A 115 PHE A 116 SITE 3 AC1 22 THR A 117 GLY A 118 VAL A 120 LEU A 123 SITE 4 AC1 22 MN A 202 MN A 203 GOL A 204 HOH A 301 SITE 5 AC1 22 HOH A 304 HOH A 310 HOH A 315 DG C 9 SITE 6 AC1 22 HOH C 101 DA D 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 4 GLU A 44 MET A 46 DGT A 201 GLY B -1 SITE 1 AC5 18 GLY B 38 SER B 39 ARG B 42 ASN B 48 SITE 2 AC5 18 ASP B 49 ASP B 51 HIS B 115 PHE B 116 SITE 3 AC5 18 THR B 117 GLY B 118 VAL B 120 LEU B 123 SITE 4 AC5 18 MN B 202 MN B 203 HOH B 305 DG F 9 SITE 5 AC5 18 HOH F 102 DA G 9 SITE 1 AC6 5 ASP B 49 ASP B 51 DGT B 201 MN B 203 SITE 2 AC6 5 HOH B 305 SITE 1 AC7 5 ASP B 49 ASP B 51 ASP B 100 DGT B 201 SITE 2 AC7 5 MN B 202 CRYST1 124.651 71.348 86.922 90.00 90.00 90.00 P 21 21 2 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 0.008022 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014016 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011505 0.00000