PDB Short entry for 5HNK HEADER HYDROLASE 18-JAN-16 5HNK TITLE CRYSTAL STRUCTURE OF T5FEN IN COMPLEX INTACT SUBSTRATE AND METAL IONS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*C)-3'); COMPND 3 CHAIN: X, Y; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: EXODEOXYRIBONUCLEASE; COMPND 7 CHAIN: A, B; COMPND 8 FRAGMENT: UNP RESIDUES 20-291; COMPND 9 SYNONYM: 5'-EXONUCLEASE,T5FEN, D15 EXONUCLEASE; COMPND 10 EC: 3.1.11.3; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: CORRESPONDS TO RESIDUES 20-291 OF UNIPROT P06229 BUT COMPND 13 WITH MUTATION D153K 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 KEYWDS HYDROLASE, ENZYME-DNA COMPLEX, FLAP ENDONUCLEASE, METALLOENZYME. EXPDTA X-RAY DIFFRACTION AUTHOR F.A.ALMALKI,M.FENG,J.ZHANG,S.E.SEDELNIKOVA,J.B.RAFFERTY,J.R.SAYERS, AUTHOR 2 P.J.ARTYMIUK REVDAT 5 10-JAN-24 5HNK 1 LINK REVDAT 4 20-JUL-16 5HNK 1 JRNL REVDAT 3 22-JUN-16 5HNK 1 JRNL REVDAT 2 08-JUN-16 5HNK 1 JRNL REVDAT 1 01-JUN-16 5HNK 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. 2.22 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) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 30073 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1595 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) : 2.22 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2045 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4407 REMARK 3 NUCLEIC ACID ATOMS : 490 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 224 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : -0.46000 REMARK 3 B33 (A**2) : 0.63000 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): 0.303 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.219 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.175 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.251 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5050 ; 0.007 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 4573 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6913 ; 1.066 ; 1.859 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10527 ; 0.947 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 542 ; 5.305 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 228 ;30.873 ;24.211 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 813 ;11.925 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;11.084 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 742 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5358 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1192 ; 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): 2174 ; 2.659 ; 3.061 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2173 ; 2.659 ; 3.060 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2714 ; 3.997 ; 4.581 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 : 4 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 12 REMARK 3 ORIGIN FOR THE GROUP (A): 11.7085 12.8422 32.2433 REMARK 3 T TENSOR REMARK 3 T11: 0.2067 T22: 0.2202 REMARK 3 T33: 0.1627 T12: -0.0295 REMARK 3 T13: -0.0251 T23: -0.0251 REMARK 3 L TENSOR REMARK 3 L11: 3.7640 L22: 0.7861 REMARK 3 L33: 3.7249 L12: -0.6540 REMARK 3 L13: 1.6212 L23: -0.1666 REMARK 3 S TENSOR REMARK 3 S11: 0.0126 S12: -0.1820 S13: -0.4294 REMARK 3 S21: 0.1044 S22: 0.1646 S23: 0.0482 REMARK 3 S31: 0.2536 S32: -0.7765 S33: -0.1772 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 : Y 1 Y 12 REMARK 3 ORIGIN FOR THE GROUP (A): 14.3976 16.3310 44.5373 REMARK 3 T TENSOR REMARK 3 T11: 0.1421 T22: 0.1491 REMARK 3 T33: 0.1407 T12: -0.0235 REMARK 3 T13: -0.0367 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 0.3145 L22: 1.3356 REMARK 3 L33: 3.6330 L12: -0.5901 REMARK 3 L13: -0.5087 L23: 1.7511 REMARK 3 S TENSOR REMARK 3 S11: 0.0261 S12: -0.0439 S13: -0.1419 REMARK 3 S21: 0.0292 S22: 0.0240 S23: 0.1763 REMARK 3 S31: 0.2294 S32: -0.1989 S33: -0.0501 REMARK 3 REMARK 3 TLS GROUP : 3 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): 17.5594 10.0648 10.2600 REMARK 3 T TENSOR REMARK 3 T11: 0.1079 T22: 0.0173 REMARK 3 T33: 0.0236 T12: -0.0032 REMARK 3 T13: 0.0084 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.9080 L22: 2.5738 REMARK 3 L33: 1.8822 L12: -0.3331 REMARK 3 L13: 0.2151 L23: 0.8113 REMARK 3 S TENSOR REMARK 3 S11: -0.0564 S12: 0.0584 S13: 0.0985 REMARK 3 S21: -0.3430 S22: 0.0197 S23: -0.1226 REMARK 3 S31: -0.3270 S32: 0.0880 S33: 0.0367 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 20 B 291 REMARK 3 ORIGIN FOR THE GROUP (A): 19.7958 29.3668 45.3881 REMARK 3 T TENSOR REMARK 3 T11: 0.0462 T22: 0.1304 REMARK 3 T33: 0.1106 T12: 0.0014 REMARK 3 T13: -0.0216 T23: 0.0214 REMARK 3 L TENSOR REMARK 3 L11: 0.4833 L22: 1.1710 REMARK 3 L33: 1.0101 L12: 0.1528 REMARK 3 L13: 0.0484 L23: 0.1033 REMARK 3 S TENSOR REMARK 3 S11: 0.1337 S12: -0.0145 S13: -0.0743 REMARK 3 S21: -0.0611 S22: -0.1206 S23: -0.0208 REMARK 3 S31: 0.0099 S32: -0.0552 S33: -0.0132 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 5HNK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000217336. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-11 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 : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : PLEASE CHECK WHICH DETECTOR WAS REMARK 200 IN PLACE AT THAT DATE REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31727 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 44.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.65400 REMARK 200 R SYM FOR SHELL (I) : 0.65400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.900 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: 1EXN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE CONCENTRATION OF BOTH REMARK 280 OLIGONUCLEOTIDES WAS ADJUSTED TO 1.1 MM FOR THE DUPLEX MOLECULE REMARK 280 BY DISSOLVING EACH ONE IN 10 MM MES PH 6.5 AND 50 MM KCL. THEY REMARK 280 WERE ANNEALED BY HEATING TO 367K FOR 10 MINUTES AND ALLOWED TO REMARK 280 COOL TO ROOM TEMPERATURE. CRYSTALS WITH OLIGONUCLEOTIDE 5OV4 REMARK 280 WERE GROWN AT 290K WITH THE D153K VARIANT OF T5FEN. THE REMARK 280 RESULTING T5FEND153K:5OV4 STRUCTURE WAS DETERMINED FROM CRYSTALS REMARK 280 GROWN IN 0.2 M MGCL2, 0.1 M BIS-TRIS BUFFER PH 5.5, 25% W/V PEG REMARK 280 3350., VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.36000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.67000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.97000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.67000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.36000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.97000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, Y, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, Y, 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 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 LEU A 100 CD2 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 PHE A 43 5.77 59.05 REMARK 500 ASP A 201 109.65 -164.31 REMARK 500 LYS B 69 62.91 -158.81 REMARK 500 ASP B 201 103.31 -161.54 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 MG Y 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC Y 6 OP1 REMARK 620 2 HOH Y 207 O 95.3 REMARK 620 3 HOH B 409 O 86.9 177.3 REMARK 620 4 HOH B 423 O 142.8 92.8 86.5 REMARK 620 5 HOH B 450 O 100.1 93.1 84.9 115.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG Y 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG Y 7 OP2 REMARK 620 2 HOH Y 205 O 88.2 REMARK 620 3 HOH Y 208 O 87.5 92.8 REMARK 620 4 HOH Y 212 O 93.1 178.7 87.2 REMARK 620 5 HOH Y 218 O 102.1 92.0 169.4 87.7 REMARK 620 6 HOH B 462 O 170.7 98.0 85.2 80.7 84.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K Y 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC Y 10 OP2 REMARK 620 2 HOH Y 211 O 71.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG Y 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG Y 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K Y 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5HML RELATED DB: PDB REMARK 900 SAME PROTEIN BUT WITHOUT BOUND DNA DBREF 5HNK X 1 12 PDB 5HNK 5HNK 1 12 DBREF 5HNK Y 1 12 PDB 5HNK 5HNK 1 12 DBREF 5HNK A 20 291 UNP P06229 EXO5_BPT5 20 291 DBREF 5HNK B 20 291 UNP P06229 EXO5_BPT5 20 291 SEQADV 5HNK LYS A 153 UNP P06229 ASP 153 ENGINEERED MUTATION SEQADV 5HNK LYS B 153 UNP P06229 ASP 153 ENGINEERED MUTATION SEQRES 1 X 12 DA DA DA DA DG DC DG DT DA DC DG DC SEQRES 1 Y 12 DA DA DA DA DG DC DG DT DA DC DG DC 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 LYS GLY ASP 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 SEQRES 1 B 272 ARG ASN LEU MET ILE VAL ASP GLY THR ASN LEU GLY PHE SEQRES 2 B 272 ARG PHE LYS HIS ASN ASN SER LYS LYS PRO PHE ALA SER SEQRES 3 B 272 SER TYR VAL SER THR ILE GLN SER LEU ALA LYS SER TYR SEQRES 4 B 272 SER ALA ARG THR THR ILE VAL LEU GLY ASP LYS GLY LYS SEQRES 5 B 272 SER VAL PHE ARG LEU GLU HIS LEU PRO GLU TYR LYS GLY SEQRES 6 B 272 ASN ARG ASP GLU LYS TYR ALA GLN ARG THR GLU GLU GLU SEQRES 7 B 272 LYS ALA LEU ASP GLU GLN PHE PHE GLU TYR LEU LYS ASP SEQRES 8 B 272 ALA PHE GLU LEU CYS LYS THR THR PHE PRO THR PHE THR SEQRES 9 B 272 ILE ARG GLY VAL GLU ALA ASP ASP MET ALA ALA TYR ILE SEQRES 10 B 272 VAL LYS LEU ILE GLY HIS LEU TYR ASP HIS VAL TRP LEU SEQRES 11 B 272 ILE SER THR LYS GLY ASP TRP ASP THR LEU LEU THR ASP SEQRES 12 B 272 LYS VAL SER ARG PHE SER PHE THR THR ARG ARG GLU TYR SEQRES 13 B 272 HIS LEU ARG ASP MET TYR GLU HIS HIS ASN VAL ASP ASP SEQRES 14 B 272 VAL GLU GLN PHE ILE SER LEU LYS ALA ILE MET GLY ASP SEQRES 15 B 272 LEU GLY ASP ASN ILE ARG GLY VAL GLU GLY ILE GLY ALA SEQRES 16 B 272 LYS ARG GLY TYR ASN ILE ILE ARG GLU PHE GLY ASN VAL SEQRES 17 B 272 LEU ASP ILE ILE ASP GLN LEU PRO LEU PRO GLY LYS GLN SEQRES 18 B 272 LYS TYR ILE GLN ASN LEU ASN ALA SER GLU GLU LEU LEU SEQRES 19 B 272 PHE ARG ASN LEU ILE LEU VAL ASP LEU PRO THR TYR CYS SEQRES 20 B 272 VAL ASP ALA ILE ALA ALA VAL GLY GLN ASP VAL LEU ASP SEQRES 21 B 272 LYS PHE THR LYS ASP ILE LEU GLU ILE ALA GLU GLN HET MG Y 101 1 HET MG Y 102 1 HET K Y 103 1 HET GOL B 301 6 HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 MG 2(MG 2+) FORMUL 7 K K 1+ FORMUL 8 GOL C3 H8 O3 FORMUL 9 HOH *224(H2 O) HELIX 1 AA1 GLY A 27 ASN A 38 1 12 HELIX 2 AA2 PHE A 43 TYR A 58 1 16 HELIX 3 AA3 SER A 72 LEU A 79 1 8 HELIX 4 AA4 LYS A 83 GLN A 92 1 10 HELIX 5 AA5 THR A 94 PHE A 119 1 26 HELIX 6 AA6 GLU A 128 GLY A 141 1 14 HELIX 7 AA7 HIS A 142 TYR A 144 5 3 HELIX 8 AA8 LYS A 153 LEU A 160 5 8 HELIX 9 AA9 HIS A 176 ARG A 178 5 3 HELIX 10 AB1 ASP A 179 ASN A 185 1 7 HELIX 11 AB2 ASP A 188 GLY A 200 1 13 HELIX 12 AB3 ASP A 201 ASN A 205 5 5 HELIX 13 AB4 GLY A 213 GLY A 225 1 13 HELIX 14 AB5 ASN A 226 GLN A 233 1 8 HELIX 15 AB6 GLN A 240 ALA A 248 1 9 HELIX 16 AB7 SER A 249 ASP A 261 1 13 HELIX 17 AB8 ASP A 261 ALA A 272 1 12 HELIX 18 AB9 GLY A 274 GLU A 290 1 17 HELIX 19 AC1 GLY B 27 PHE B 32 1 6 HELIX 20 AC2 ARG B 33 LYS B 35 5 3 HELIX 21 AC3 PHE B 43 TYR B 58 1 16 HELIX 22 AC4 SER B 72 LEU B 79 1 8 HELIX 23 AC5 ASN B 85 GLN B 92 1 8 HELIX 24 AC6 THR B 94 THR B 117 1 24 HELIX 25 AC7 GLU B 128 GLY B 141 1 14 HELIX 26 AC8 HIS B 142 TYR B 144 5 3 HELIX 27 AC9 LYS B 153 LEU B 160 5 8 HELIX 28 AD1 HIS B 176 ARG B 178 5 3 HELIX 29 AD2 ASP B 179 ASN B 185 1 7 HELIX 30 AD3 ASP B 188 GLY B 200 1 13 HELIX 31 AD4 ASP B 201 ASN B 205 5 5 HELIX 32 AD5 GLY B 213 GLY B 225 1 13 HELIX 33 AD6 ASN B 226 LEU B 234 1 9 HELIX 34 AD7 GLN B 240 ALA B 248 1 9 HELIX 35 AD8 SER B 249 ASP B 261 1 13 HELIX 36 AD9 ASP B 261 ALA B 272 1 12 HELIX 37 AE1 GLY B 274 GLN B 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 MET A 23 O THR A 62 SHEET 4 AA1 6 HIS A 146 ILE A 150 1 O TRP A 148 N LEU A 22 SHEET 5 AA1 6 VAL A 164 PHE A 167 1 O SER A 165 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 6 THR B 121 PHE B 122 0 SHEET 2 AA2 6 ALA B 60 LEU B 66 1 N VAL B 65 O PHE B 122 SHEET 3 AA2 6 ASN B 21 ASP B 26 1 N MET B 23 O ILE B 64 SHEET 4 AA2 6 VAL B 147 ILE B 150 1 O ILE B 150 N ILE B 24 SHEET 5 AA2 6 VAL B 164 PHE B 167 1 O PHE B 167 N LEU B 149 SHEET 6 AA2 6 GLU B 174 TYR B 175 -1 O TYR B 175 N ARG B 166 LINK OP1 DC Y 6 MG MG Y 101 1555 1555 1.96 LINK OP2 DG Y 7 MG MG Y 102 1555 1555 2.09 LINK OP2 DC Y 10 K K Y 103 1555 1555 2.43 LINK MG MG Y 101 O HOH Y 207 1555 1555 1.94 LINK MG MG Y 101 O HOH B 409 1555 1555 2.25 LINK MG MG Y 101 O HOH B 423 1555 1555 2.09 LINK MG MG Y 101 O HOH B 450 1555 1555 2.17 LINK MG MG Y 102 O HOH Y 205 1555 1555 2.05 LINK MG MG Y 102 O HOH Y 208 1555 1555 2.10 LINK MG MG Y 102 O HOH Y 212 1555 1555 2.27 LINK MG MG Y 102 O HOH Y 218 1555 1555 2.10 LINK MG MG Y 102 O HOH B 462 1555 1555 2.35 LINK K K Y 103 O HOH Y 211 1555 1555 2.66 CISPEP 1 LEU A 234 PRO A 235 0 2.77 CISPEP 2 LEU B 234 PRO B 235 0 -1.44 SITE 1 AC1 5 HOH B 409 HOH B 423 HOH B 450 DC Y 6 SITE 2 AC1 5 HOH Y 207 SITE 1 AC2 6 HOH B 462 DG Y 7 HOH Y 205 HOH Y 208 SITE 2 AC2 6 HOH Y 212 HOH Y 218 SITE 1 AC3 4 MET A 199 VAL A 209 DC Y 10 HOH Y 211 SITE 1 AC4 5 ASP B 87 LYS B 280 ASP B 284 DA Y 1 SITE 2 AC4 5 DA Y 3 CRYST1 44.720 109.940 127.340 90.00 90.00 90.00 P 21 21 21 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 0.022361 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009096 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007853 0.00000