PDB Short entry for 5HP4 HEADER HYDROLASE 20-JAN-16 5HP4 TITLE CRYSTAL STRUCTURE BACTERIOHAGE T5 D15 FLAP ENDONUCLEASE (D155K) TITLE 2 PSEUDO-ENZYME-PRODUCT COMPLEX WITH DNA AND METAL IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*G)-3'); COMPND 4 CHAIN: X; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: OLIGONUCLEOTIDE FORMS IMPERFECT HELICAL DUPLEX WITH 3' COMPND 7 OVERHANG WHEN ANNEALED.; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: EXODEOXYRIBONUCLEASE; COMPND 10 CHAIN: A; COMPND 11 FRAGMENT: UNP RESIDUES 20-291; COMPND 12 SYNONYM: 5'-EXONUCLEASE,T5FEN; COMPND 13 EC: 3.1.11.3; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES; COMPND 16 OTHER_DETAILS: THE EXPRESSED RECOMBINANT CORRESPONDED TO RESIDUES 20- COMPND 17 291 OF THE PROTEIN WITH A D155K SUBSTITUTION. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE T5; SOURCE 7 ORGANISM_TAXID: 10726; SOURCE 8 GENE: D15; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: M72; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PJONEX4 DERIVATIVE KEYWDS ENZYME-SUBSTRATE-COMPLEX, FLAP ENDONUCLEASE, METALLOENZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.A.ALMALKI,J.ZHANG,S.E.SEDELNIKOVA,J.B.RAFFERTY,J.R.SAYERS, AUTHOR 2 P.A.ARTYMIUK REVDAT 5 10-JAN-24 5HP4 1 LINK REVDAT 4 20-JUL-16 5HP4 1 JRNL REVDAT 3 22-JUN-16 5HP4 1 JRNL REVDAT 2 08-JUN-16 5HP4 1 JRNL REVDAT 1 01-JUN-16 5HP4 0 JRNL AUTH F.A.ALMALKI,C.S.FLEMMING,J.ZHANG,M.FENG,S.E.SEDELNIKOVA, JRNL AUTH 2 T.CESKA,J.B.RAFFERTY,J.R.SAYERS,P.J.ARTYMIUK JRNL TITL DIRECT OBSERVATION OF DNA THREADING IN FLAP ENDONUCLEASE JRNL TITL 2 COMPLEXES. JRNL REF NAT.STRUCT.MOL.BIOL. V. 23 640 2016 JRNL REFN ESSN 1545-9985 JRNL PMID 27273516 JRNL DOI 10.1038/NSMB.3241 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 35532 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1871 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2575 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 139 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2194 REMARK 3 NUCLEIC ACID ATOMS : 345 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 218 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.15000 REMARK 3 B22 (A**2) : 1.15000 REMARK 3 B33 (A**2) : -2.29000 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): 0.101 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.100 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.388 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2635 ; 0.010 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 2336 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3629 ; 1.371 ; 1.830 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5386 ; 1.030 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 273 ; 4.937 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;31.008 ;24.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 402 ;13.563 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;11.674 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 387 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2738 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 606 ; 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): 1092 ; 5.341 ; 2.426 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1091 ; 5.019 ; 2.418 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1365 ; 5.717 ; 3.606 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : X 1 X 17 REMARK 3 ORIGIN FOR THE GROUP (A): -19.4541 -11.0449 -9.2797 REMARK 3 T TENSOR REMARK 3 T11: 0.1326 T22: 0.0856 REMARK 3 T33: 0.2018 T12: -0.0044 REMARK 3 T13: -0.0358 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 0.1310 L22: 0.0262 REMARK 3 L33: 0.7683 L12: -0.0231 REMARK 3 L13: -0.0413 L23: 0.1028 REMARK 3 S TENSOR REMARK 3 S11: 0.0593 S12: -0.0752 S13: 0.0142 REMARK 3 S21: -0.0056 S22: 0.0147 S23: 0.0332 REMARK 3 S31: 0.0810 S32: 0.0480 S33: -0.0741 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 20 A 291 REMARK 3 ORIGIN FOR THE GROUP (A): -5.4856 -18.8612 -17.4401 REMARK 3 T TENSOR REMARK 3 T11: 0.0400 T22: 0.0290 REMARK 3 T33: 0.0305 T12: -0.0001 REMARK 3 T13: -0.0152 T23: -0.0214 REMARK 3 L TENSOR REMARK 3 L11: 0.7120 L22: 0.9146 REMARK 3 L33: 0.6664 L12: 0.0266 REMARK 3 L13: 0.2435 L23: -0.1275 REMARK 3 S TENSOR REMARK 3 S11: 0.0221 S12: -0.0028 S13: 0.0276 REMARK 3 S21: -0.0483 S22: 0.0213 S23: 0.0046 REMARK 3 S31: -0.0255 S32: 0.1116 S33: -0.0434 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5HP4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000217415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37488 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.861 REMARK 200 RESOLUTION RANGE LOW (A) : 67.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 27.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 28.80 REMARK 200 R MERGE FOR SHELL (I) : 1.04300 REMARK 200 R SYM FOR SHELL (I) : 1.04300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.600 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: 5HML REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: OLIGONUCLEOTIDES WAS ADJUSTED TO 1.1 REMARK 280 MM FOR THE DUPLEX MOLECULE BY DISSOLVING EACH ONE IN 10 MM MES REMARK 280 PH 6.5 AND 50 MM KCL. T5FEND155K WITH OLIGONUCLEOTIDE 3OV6 REMARK 280 PREPARED ABOVE, GREW IN 0.2 M CACL2, 0.1 M SODIUM ACETATE BUFFER REMARK 280 PH 5, 20% W/V PEG 6000., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 93.90500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.75500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.75500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 140.85750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.75500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.75500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.95250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.75500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.75500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 140.85750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.75500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.75500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.95250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 93.90500 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: X REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -33.75500 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -33.75500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -46.95250 REMARK 350 APPLY THE FOLLOWING TO CHAINS: X REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 ARG A 20 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 202 CD1 REMARK 470 GLN A 291 CG CD OE1 NE2 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 DG X 16 O5' - P - OP2 ANGL. DEV. = -7.1 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 LYS A 69 81.90 -152.41 REMARK 500 LEU A 79 89.68 -158.64 REMARK 500 LYS A 83 16.56 57.13 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 NA X 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC X 4 O2 REMARK 620 2 DT X 5 O4' 92.9 REMARK 620 3 DT X 7 O2 83.2 62.3 REMARK 620 4 HOH X 231 O 88.8 74.7 14.2 REMARK 620 5 HOH X 234 O 77.9 70.3 9.1 12.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K X 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT X 5 OP1 REMARK 620 2 DT X 5 OP2 47.5 REMARK 620 3 HOH X 224 O 104.8 57.5 REMARK 620 4 VAL A 209 O 79.1 118.7 143.9 REMARK 620 5 ILE A 212 O 95.2 78.0 64.1 79.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA X 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC X 15 O2 REMARK 620 2 HOH X 216 O 82.6 REMARK 620 3 HOH X 220 O 80.5 72.0 REMARK 620 4 HOH X 221 O 76.1 145.6 77.9 REMARK 620 5 HOH X 223 O 72.2 82.0 144.4 115.8 REMARK 620 6 HOH X 236 O 126.5 139.9 133.0 74.0 82.4 REMARK 620 7 HOH A 557 O 148.2 94.7 68.7 89.7 139.0 74.2 REMARK 620 8 HOH A 570 O 134.7 75.5 127.0 137.9 65.9 64.4 73.7 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 128 OE1 REMARK 620 2 GLU A 128 OE2 49.5 REMARK 620 3 ASP A 130 OD1 95.8 70.7 REMARK 620 4 HOH A 405 O 82.0 100.8 169.8 REMARK 620 5 HOH A 413 O 159.4 145.4 82.8 102.7 REMARK 620 6 HOH A 430 O 125.6 87.0 97.9 75.6 74.8 REMARK 620 7 HOH A 522 O 85.5 134.0 112.1 77.7 76.2 134.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA X 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA X 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K X 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5HNK RELATED DB: PDB REMARK 900 PROTEIN WITH MUTATION AT D153K WITH SUBSTRATE DNA DBREF 5HP4 X 1 17 PDB 5HP4 5HP4 1 17 DBREF 5HP4 A 20 291 UNP P06229 EXO5_BPT5 20 291 SEQADV 5HP4 LYS A 155 UNP P06229 ASP 155 ENGINEERED MUTATION SEQRES 1 X 17 DG DA DT DC DT DA DT DA DT DG DC DC DA SEQRES 2 X 17 DT DC DG DG SEQRES 1 A 272 ARG ASN LEU MET ILE VAL ASP GLY THR ASN LEU GLY PHE SEQRES 2 A 272 ARG PHE LYS HIS ASN ASN SER LYS LYS PRO PHE ALA SER SEQRES 3 A 272 SER TYR VAL SER THR ILE GLN SER LEU ALA LYS SER TYR SEQRES 4 A 272 SER ALA ARG THR THR ILE VAL LEU GLY ASP LYS GLY LYS SEQRES 5 A 272 SER VAL PHE ARG LEU GLU HIS LEU PRO GLU TYR LYS GLY SEQRES 6 A 272 ASN ARG ASP GLU LYS TYR ALA GLN ARG THR GLU GLU GLU SEQRES 7 A 272 LYS ALA LEU ASP GLU GLN PHE PHE GLU TYR LEU LYS ASP SEQRES 8 A 272 ALA PHE GLU LEU CYS LYS THR THR PHE PRO THR PHE THR SEQRES 9 A 272 ILE ARG GLY VAL GLU ALA ASP ASP MET ALA ALA TYR ILE SEQRES 10 A 272 VAL LYS LEU ILE GLY HIS LEU TYR ASP HIS VAL TRP LEU SEQRES 11 A 272 ILE SER THR ASP GLY LYS TRP ASP THR LEU LEU THR ASP SEQRES 12 A 272 LYS VAL SER ARG PHE SER PHE THR THR ARG ARG GLU TYR SEQRES 13 A 272 HIS LEU ARG ASP MET TYR GLU HIS HIS ASN VAL ASP ASP SEQRES 14 A 272 VAL GLU GLN PHE ILE SER LEU LYS ALA ILE MET GLY ASP SEQRES 15 A 272 LEU GLY ASP ASN ILE ARG GLY VAL GLU GLY ILE GLY ALA SEQRES 16 A 272 LYS ARG GLY TYR ASN ILE ILE ARG GLU PHE GLY ASN VAL SEQRES 17 A 272 LEU ASP ILE ILE ASP GLN LEU PRO LEU PRO GLY LYS GLN SEQRES 18 A 272 LYS TYR ILE GLN ASN LEU ASN ALA SER GLU GLU LEU LEU SEQRES 19 A 272 PHE ARG ASN LEU ILE LEU VAL ASP LEU PRO THR TYR CYS SEQRES 20 A 272 VAL ASP ALA ILE ALA ALA VAL GLY GLN ASP VAL LEU ASP SEQRES 21 A 272 LYS PHE THR LYS ASP ILE LEU GLU ILE ALA GLU GLN HET CA X 101 1 HET NA X 102 1 HET K X 103 1 HET CA A 301 1 HET GOL A 302 6 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CA 2(CA 2+) FORMUL 4 NA NA 1+ FORMUL 5 K K 1+ FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *218(H2 O) HELIX 1 AA1 GLY A 27 PHE A 32 1 6 HELIX 2 AA2 ARG A 33 LYS A 35 5 3 HELIX 3 AA3 PHE A 43 TYR A 58 1 16 HELIX 4 AA4 SER A 72 LEU A 79 1 8 HELIX 5 AA5 LYS A 83 GLN A 92 1 10 HELIX 6 AA6 THR A 94 PHE A 119 1 26 HELIX 7 AA7 GLU A 128 GLY A 141 1 14 HELIX 8 AA8 HIS A 142 TYR A 144 5 3 HELIX 9 AA9 ASP A 153 LEU A 160 5 8 HELIX 10 AB1 HIS A 176 ARG A 178 5 3 HELIX 11 AB2 ASP A 179 ASN A 185 1 7 HELIX 12 AB3 ASP A 188 MET A 199 1 12 HELIX 13 AB4 LEU A 202 ASN A 205 5 4 HELIX 14 AB5 GLY A 213 GLY A 225 1 13 HELIX 15 AB6 ASN A 226 GLN A 233 1 8 HELIX 16 AB7 GLN A 240 ALA A 248 1 9 HELIX 17 AB8 SER A 249 ASP A 261 1 13 HELIX 18 AB9 ASP A 261 ALA A 272 1 12 HELIX 19 AC1 GLY A 274 GLN A 291 1 18 SHEET 1 AA1 6 THR A 121 PHE A 122 0 SHEET 2 AA1 6 ALA A 60 LEU A 66 1 N VAL A 65 O PHE A 122 SHEET 3 AA1 6 ASN A 21 ASP A 26 1 N VAL A 25 O ILE A 64 SHEET 4 AA1 6 VAL A 147 ILE A 150 1 O TRP A 148 N LEU A 22 SHEET 5 AA1 6 VAL A 164 PHE A 167 1 O PHE A 167 N LEU A 149 SHEET 6 AA1 6 GLU A 174 TYR A 175 -1 O TYR A 175 N ARG A 166 SHEET 1 AA2 2 GLY A 200 ASP A 201 0 SHEET 2 AA2 2 ILE A 206 ARG A 207 -1 O ILE A 206 N ASP A 201 LINK O2 DC X 4 NA NA X 102 1555 7555 2.29 LINK O4' DT X 5 NA NA X 102 1555 7555 2.55 LINK OP1 DT X 5 K K X 103 1555 1555 3.16 LINK OP2 DT X 5 K K X 103 1555 1555 3.22 LINK O2 DT X 7 NA NA X 102 1555 1555 2.23 LINK O2 DC X 15 CA CA X 101 1555 1555 2.41 LINK CA CA X 101 O HOH X 216 1555 1555 2.50 LINK CA CA X 101 O HOH X 220 1555 1555 2.57 LINK CA CA X 101 O HOH X 221 1555 1555 2.53 LINK CA CA X 101 O HOH X 223 1555 1555 2.41 LINK CA CA X 101 O HOH X 236 1555 1555 2.58 LINK CA CA X 101 O HOH A 557 1555 5454 2.37 LINK CA CA X 101 O HOH A 570 1555 5454 2.63 LINK NA NA X 102 O HOH X 231 1555 7555 2.70 LINK NA NA X 102 O HOH X 234 1555 7555 2.23 LINK K K X 103 O HOH X 224 1555 1555 2.64 LINK K K X 103 O VAL A 209 1555 1555 2.88 LINK K K X 103 O ILE A 212 1555 1555 2.94 LINK OE1 GLU A 128 CA CA A 301 1555 1555 2.55 LINK OE2 GLU A 128 CA CA A 301 1555 1555 2.63 LINK OD1 ASP A 130 CA CA A 301 1555 1555 2.48 LINK CA CA A 301 O HOH A 405 1555 1555 2.39 LINK CA CA A 301 O HOH A 413 1555 1555 2.34 LINK CA CA A 301 O HOH A 430 1555 1555 2.34 LINK CA CA A 301 O HOH A 522 1555 1555 2.45 CISPEP 1 LEU A 234 PRO A 235 0 -3.75 SITE 1 AC1 8 HOH A 557 HOH A 570 DC X 15 HOH X 216 SITE 2 AC1 8 HOH X 220 HOH X 221 HOH X 223 HOH X 236 SITE 1 AC2 6 DC X 4 DT X 5 DT X 7 DA X 8 SITE 2 AC2 6 HOH X 231 HOH X 234 SITE 1 AC3 5 MET A 199 VAL A 209 ILE A 212 DT X 5 SITE 2 AC3 5 HOH X 224 SITE 1 AC4 6 GLU A 128 ASP A 130 HOH A 405 HOH A 413 SITE 2 AC4 6 HOH A 430 HOH A 522 SITE 1 AC5 4 THR A 28 ASP A 68 PHE A 112 THR A 123 CRYST1 67.510 67.510 187.810 90.00 90.00 90.00 P 43 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 0.014813 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014813 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005325 0.00000