HEADER TRANSFERASE/DNA 17-NOV-17 5YTF TITLE STRUCTURE OF LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS TITLE 2 HOST-GUEST COMPLEX WITH THE UNNATURAL BASE M-FC PAIR WITH DA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LARGE FRAGMENT; COMPND 5 SYNONYM: TAQ POLYMERASE 1; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*AP*AP*AP*CP*GP*GP*CP*GP*CP*CP*GP*(92F) COMPND 14 P*GP*GP*TP*C)-3'); COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POLA, POL1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, HOST-GUEST COMPLEX, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.ZENG,M.MONDAL,R.Y.SONG,J.ZHANG,B.XIA,Y.Q.GAO,C.Q.YI REVDAT 4 22-NOV-23 5YTF 1 REMARK REVDAT 3 22-JUN-22 5YTF 1 LINK REVDAT 2 02-JAN-19 5YTF 1 JRNL REVDAT 1 21-NOV-18 5YTF 0 JRNL AUTH H.ZENG,M.MONDAL,R.SONG,J.ZHANG,B.XIA,M.LIU,C.ZHU,B.HE, JRNL AUTH 2 Y.Q.GAO,C.YI JRNL TITL UNNATURAL CYTOSINE BASES RECOGNIZED AS THYMINES BY DNA JRNL TITL 2 POLYMERASES BY THE FORMATION OF THE WATSON-CRICK GEOMETRY. JRNL REF ANGEW. CHEM. INT. ED. ENGL. V. 58 130 2019 JRNL REFN ESSN 1521-3773 JRNL PMID 30407705 JRNL DOI 10.1002/ANIE.201807845 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 93.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 40333 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2127 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2989 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE SET COUNT : 145 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4278 REMARK 3 NUCLEIC ACID ATOMS : 572 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 358 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : 0.58000 REMARK 3 B33 (A**2) : -1.88000 REMARK 3 B12 (A**2) : 0.29000 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): 0.190 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.169 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.526 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5069 ; 0.013 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 4634 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6992 ; 1.768 ; 1.893 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10649 ; 1.219 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 546 ;10.238 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 207 ;33.191 ;22.367 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 767 ;15.845 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 54 ;18.856 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 743 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5297 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1173 ; 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): 2163 ; 0.830 ; 1.974 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2162 ; 0.827 ; 1.973 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2704 ; 1.307 ; 2.956 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2705 ; 1.307 ; 2.957 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2905 ; 1.108 ; 2.238 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2905 ; 1.108 ; 2.238 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4285 ; 1.791 ; 3.313 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6283 ; 3.318 ;17.890 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6283 ; 3.318 ;17.890 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 294 A 832 REMARK 3 RESIDUE RANGE : A 901 A 902 REMARK 3 ORIGIN FOR THE GROUP (A): -34.9520 -12.7487 6.7065 REMARK 3 T TENSOR REMARK 3 T11: 0.0370 T22: 0.0217 REMARK 3 T33: 0.0461 T12: -0.0054 REMARK 3 T13: 0.0212 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 0.9914 L22: 0.9112 REMARK 3 L33: 1.2918 L12: -0.2198 REMARK 3 L13: 0.1299 L23: -0.2104 REMARK 3 S TENSOR REMARK 3 S11: 0.0303 S12: -0.0733 S13: 0.0316 REMARK 3 S21: 0.0945 S22: 0.0028 S23: -0.0156 REMARK 3 S31: -0.0986 S32: 0.1050 S33: -0.0331 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 5YTF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300005843. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 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 : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40333 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 93.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 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: 4DFK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M SODIUM CACODYLATE (PH 7.0), 0.2 REMARK 280 M AMMONIUM ACETATE, 0.01 M MAGNESIUM ACETATE, 30% PEG 8000, REMARK 280 EVAPORATION, TEMPERATURE 293.15K 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 30.10633 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 60.21267 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 60.21267 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 30.10633 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 GLU A 530 CG CD OE1 OE2 REMARK 470 GLU A 832 CG CD OE1 OE2 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 GLN A 680 CB ALA A 683 1.98 REMARK 500 C GLN A 680 CB ALA A 683 2.09 REMARK 500 NE ARG A 587 O HOH A 1001 2.18 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 1235 O HOH A 1235 4555 1.52 REMARK 500 O HOH A 1084 O HOH C 332 3444 1.78 REMARK 500 O HOH A 1140 O HOH A 1140 4555 1.81 REMARK 500 O HOH A 1270 O HOH A 1270 5554 1.85 REMARK 500 O HOH A 1230 O HOH A 1239 6445 1.86 REMARK 500 OE2 GLU A 421 O HOH A 1243 6455 2.06 REMARK 500 O HOH A 1193 O HOH A 1292 4555 2.07 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 DC B 111 O3' DOC B 112 P 0.076 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 PRO A 300 C - N - CD ANGL. DEV. = -17.9 DEGREES REMARK 500 ARG A 343 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 349 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 349 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 536 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 559 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 559 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 PRO A 579 C - N - CD ANGL. DEV. = 15.1 DEGREES REMARK 500 ARG A 596 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA C 201 C5' - C4' - O4' ANGL. DEV. = 9.3 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 ASP A 381 112.34 -166.38 REMARK 500 TYR A 545 -57.51 -128.59 REMARK 500 VAL A 586 -18.57 -159.05 REMARK 500 ILE A 684 -110.76 -132.70 REMARK 500 TYR A 686 1.39 -61.12 REMARK 500 GLU A 687 -72.65 -82.02 REMARK 500 ALA A 691 -42.47 78.12 REMARK 500 HIS A 784 -60.30 68.98 REMARK 500 TYR A 811 89.45 -165.25 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 TRP A 299 PRO A 300 60.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TRP A 299 11.85 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 A1300 DISTANCE = 5.84 ANGSTROMS 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 MG A 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 80.8 REMARK 620 3 ASP A 785 OD2 86.0 87.1 REMARK 620 4 DGT A 903 O3G 88.8 88.2 173.5 REMARK 620 5 DGT A 903 O2B 170.8 90.6 96.5 88.0 REMARK 620 6 DGT A 903 O2A 99.0 178.4 91.4 93.4 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 ASP A 785 OD1 112.8 REMARK 620 3 DGT A 903 O2A 99.8 84.0 REMARK 620 4 HOH A1063 O 103.6 92.6 155.8 REMARK 620 5 HOH A1122 O 89.1 155.3 81.1 93.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 303 O REMARK 620 2 HOH B 306 O 95.0 REMARK 620 3 HOH B 308 O 104.0 97.4 REMARK 620 4 HOH B 325 O 89.5 80.1 166.4 REMARK 620 5 HOH B 326 O 173.2 86.9 82.1 84.4 REMARK 620 6 HOH C 330 O 94.9 168.3 86.2 93.8 82.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DGT A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 DBREF 5YTF A 294 832 UNP P19821 DPO1_THEAQ 294 832 DBREF 5YTF B 101 112 PDB 5YTF 5YTF 101 112 DBREF 5YTF C 201 216 PDB 5YTF 5YTF 201 216 SEQRES 1 A 539 LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY ALA PHE SEQRES 2 A 539 VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET TRP ALA SEQRES 3 A 539 ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY ARG VAL SEQRES 4 A 539 HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG ASP LEU SEQRES 5 A 539 LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SER VAL SEQRES 6 A 539 LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO GLY ASP SEQRES 7 A 539 ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SER ASN SEQRES 8 A 539 THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY GLY GLU SEQRES 9 A 539 TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SER GLU SEQRES 10 A 539 ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU GLY GLU SEQRES 11 A 539 GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU ARG PRO SEQRES 12 A 539 LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR GLY VAL SEQRES 13 A 539 ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER LEU GLU SEQRES 14 A 539 VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU VAL PHE SEQRES 15 A 539 ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER ARG ASP SEQRES 16 A 539 GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY LEU PRO SEQRES 17 A 539 ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SER THR SEQRES 18 A 539 SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA HIS PRO SEQRES 19 A 539 ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU THR LYS SEQRES 20 A 539 LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP LEU ILE SEQRES 21 A 539 HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE ASN GLN SEQRES 22 A 539 THR ALA THR ALA THR GLY ARG LEU SER SER SER ASP PRO SEQRES 23 A 539 ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU GLY GLN SEQRES 24 A 539 ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY TRP LEU SEQRES 25 A 539 LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU ARG VAL SEQRES 26 A 539 LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE ARG VAL SEQRES 27 A 539 PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR ALA SER SEQRES 28 A 539 TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP PRO LEU SEQRES 29 A 539 MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY VAL LEU SEQRES 30 A 539 TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU LEU ALA SEQRES 31 A 539 ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU ARG TYR SEQRES 32 A 539 PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE GLU LYS SEQRES 33 A 539 THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL GLU THR SEQRES 34 A 539 LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU GLU ALA SEQRES 35 A 539 ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG MET ALA SEQRES 36 A 539 PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP LEU MET SEQRES 37 A 539 LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU GLU GLU SEQRES 38 A 539 MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP GLU LEU SEQRES 39 A 539 VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA VAL ALA SEQRES 40 A 539 ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR PRO LEU SEQRES 41 A 539 ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY GLU ASP SEQRES 42 A 539 TRP LEU SER ALA LYS GLU SEQRES 1 B 12 DG DA DC DC DA DC DG DG DC DG DC DOC SEQRES 1 C 16 DA DA DA DC DG DG DC DG DC DC DG 92F DG SEQRES 2 C 16 DG DT DC HET DOC B 112 18 HET 92F C 212 25 HET MG A 901 1 HET MG A 902 1 HET DGT A 903 31 HET GOL A 904 6 HET MG B 201 1 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM 92F 7-AMINO-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 92F PENTOFURANOSYL)-2-OXO-2,3-DIHYDROPYRIDO[2,3- HETNAM 3 92F D]PYRIMIDINE-6-CARBONITRILE HETNAM MG MAGNESIUM ION HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 3 92F C13 H14 N5 O7 P FORMUL 4 MG 3(MG 2+) FORMUL 6 DGT C10 H16 N5 O13 P3 FORMUL 7 GOL C3 H8 O3 FORMUL 9 HOH *358(H2 O) HELIX 1 AA1 GLU A 337 LEU A 342 1 6 HELIX 2 AA2 ARG A 343 LEU A 345 5 3 HELIX 3 AA3 LEU A 352 GLU A 363 1 12 HELIX 4 AA4 ASP A 372 ASP A 381 1 10 HELIX 5 AA5 THR A 386 GLY A 395 1 10 HELIX 6 AA6 GLU A 401 LEU A 420 1 20 HELIX 7 AA7 GLU A 423 VAL A 433 1 11 HELIX 8 AA8 VAL A 433 GLY A 448 1 16 HELIX 9 AA9 ASP A 452 GLY A 479 1 28 HELIX 10 AB1 SER A 486 ASP A 496 1 11 HELIX 11 AB2 SER A 515 ARG A 523 1 9 HELIX 12 AB3 PRO A 527 TYR A 545 1 19 HELIX 13 AB4 PRO A 548 ILE A 553 5 6 HELIX 14 AB5 THR A 588 ARG A 596 1 9 HELIX 15 AB6 GLN A 613 GLY A 624 1 12 HELIX 16 AB7 ASP A 625 GLU A 634 1 10 HELIX 17 AB8 ASP A 637 GLY A 648 1 12 HELIX 18 AB9 PRO A 650 VAL A 654 5 5 HELIX 19 AC1 ASP A 655 TYR A 671 1 17 HELIX 20 AC2 SER A 674 ALA A 683 1 10 HELIX 21 AC3 ALA A 691 PHE A 700 1 10 HELIX 22 AC4 PHE A 700 GLY A 718 1 19 HELIX 23 AC5 PRO A 731 ALA A 735 5 5 HELIX 24 AC6 VAL A 737 GLY A 776 1 40 HELIX 25 AC7 ARG A 795 GLY A 809 1 15 SHEET 1 AA1 4 GLU A 295 ALA A 297 0 SHEET 2 AA1 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 AA1 4 LEU A 321 ARG A 328 -1 N ALA A 326 O HIS A 333 SHEET 4 AA1 4 PHE A 306 LEU A 311 -1 N PHE A 306 O ALA A 327 SHEET 1 AA2 2 ARG A 450 LEU A 451 0 SHEET 2 AA2 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 AA3 2 ARG A 563 ASN A 565 0 SHEET 2 AA3 2 SER A 575 SER A 577 -1 O SER A 577 N ARG A 563 SHEET 1 AA4 4 ARG A 778 GLN A 782 0 SHEET 2 AA4 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 AA4 4 TRP A 604 TYR A 611 -1 N LEU A 605 O ALA A 791 SHEET 4 AA4 4 VAL A 819 GLY A 824 -1 O GLY A 822 N ALA A 608 SHEET 1 AA5 2 TYR A 719 GLU A 721 0 SHEET 2 AA5 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK O3' DC B 111 P DOC B 112 1555 1555 1.68 LINK O3' DG C 211 P 92F C 212 1555 1555 1.59 LINK O3' 92F C 212 P DG C 213 1555 1555 1.59 LINK OD1 ASP A 610 MG MG A 901 1555 1555 2.16 LINK OD2 ASP A 610 MG MG A 902 1555 1555 2.24 LINK O TYR A 611 MG MG A 901 1555 1555 2.09 LINK OD2 ASP A 785 MG MG A 901 1555 1555 2.13 LINK OD1 ASP A 785 MG MG A 902 1555 1555 2.25 LINK MG MG A 901 O3G DGT A 903 1555 1555 2.05 LINK MG MG A 901 O2B DGT A 903 1555 1555 2.05 LINK MG MG A 901 O2A DGT A 903 1555 1555 2.09 LINK MG MG A 902 O2A DGT A 903 1555 1555 2.41 LINK MG MG A 902 O HOH A1063 1555 1555 2.29 LINK MG MG A 902 O HOH A1122 1555 1555 2.46 LINK MG MG B 201 O HOH B 303 1555 1555 1.91 LINK MG MG B 201 O HOH B 306 1555 1555 1.95 LINK MG MG B 201 O HOH B 308 1555 1555 1.95 LINK MG MG B 201 O HOH B 325 1555 1555 2.06 LINK MG MG B 201 O HOH B 326 1555 1555 2.25 LINK MG MG B 201 O HOH C 330 1555 1555 2.05 CISPEP 1 ASP A 578 PRO A 579 0 0.92 CISPEP 2 LEU A 682 ALA A 683 0 -4.81 SITE 1 AC1 5 ASP A 610 TYR A 611 ASP A 785 MG A 902 SITE 2 AC1 5 DGT A 903 SITE 1 AC2 7 ASP A 610 ASP A 785 MG A 901 DGT A 903 SITE 2 AC2 7 HOH A1063 HOH A1122 DOC B 112 SITE 1 AC3 24 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC3 24 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC3 24 ARG A 659 ARG A 660 LYS A 663 PHE A 667 SITE 4 AC3 24 TYR A 671 ASP A 785 MG A 901 MG A 902 SITE 5 AC3 24 HOH A1071 HOH A1074 HOH A1086 HOH A1103 SITE 6 AC3 24 HOH A1122 DOC B 112 DC C 204 DG C 205 SITE 1 AC4 3 TRP A 428 PHE A 724 HOH A1015 SITE 1 AC5 6 HOH B 303 HOH B 306 HOH B 308 HOH B 325 SITE 2 AC5 6 HOH B 326 HOH C 330 CRYST1 107.690 107.690 90.319 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 0.009286 0.005361 0.000000 0.00000 SCALE2 0.000000 0.010722 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011072 0.00000