HEADER HYDROLASE/DNA 06-SEP-10 3OR3 TITLE RESTRICTION ENDONUCLEASE HPY188I IN COMPLEX WITH PRODUCT DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RESTRICTION ENDONUCLEASE HPY188I; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*AP*TP*CP*T)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(*GP*TP*TP*CP*A)-3'; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: 5'-D(P*GP*AP*AP*C)-3'; COMPND 15 CHAIN: E; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: 5'-D(P*GP*AP*TP*C)-3'; COMPND 19 CHAIN: F; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_COMMON: CAMPYLOBACTER PYLORI; SOURCE 4 ORGANISM_TAXID: 585532; SOURCE 5 STRAIN: 188; SOURCE 6 GENE: HPY188IR, SYNTHETIC GENE CODON OPTIMIZED FOR ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET15BMOD; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE; SOURCE 21 MOL_ID: 5; SOURCE 22 SYNTHETIC: YES; SOURCE 23 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE KEYWDS ENDONUCLEASE-DNA COMPLEX, RESTRICTION ENZYME, HPY188I, INTERCALATION, KEYWDS 2 GIY-YIG NUCLEASE, CATALYTIC MECHANISM, PSEUDOPALINDROME, HYDROLASE- KEYWDS 3 DNA COMPLEX, RESTRICTION ENDONUCLEASE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.SOKOLOWSKA,H.CZAPINSKA,M.BOCHTLER REVDAT 4 08-NOV-17 3OR3 1 REMARK REVDAT 3 06-APR-11 3OR3 1 JRNL REVDAT 2 05-JAN-11 3OR3 1 JRNL REVDAT 1 20-OCT-10 3OR3 0 JRNL AUTH M.SOKOLOWSKA,H.CZAPINSKA,M.BOCHTLER JRNL TITL HPY188I-DNA PRE- AND POST-CLEAVAGE COMPLEXES--SNAPSHOTS OF JRNL TITL 2 THE GIY-YIG NUCLEASE MEDIATED CATALYSIS. JRNL REF NUCLEIC ACIDS RES. V. 39 1554 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 20935048 JRNL DOI 10.1093/NAR/GKQ821 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 35323 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RESOLUTION SHELLS REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1723 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4717 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE SET COUNT : 213 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2844 REMARK 3 NUCLEIC ACID ATOMS : 365 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 311 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.39000 REMARK 3 B22 (A**2) : 0.39000 REMARK 3 B33 (A**2) : -0.78000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.143 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.401 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4158 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2639 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5809 ; 1.281 ; 2.183 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6573 ; 3.943 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 438 ; 5.795 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;37.888 ;26.213 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 668 ;14.622 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;13.470 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 628 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4258 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 728 ; 0.007 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 748 ; 0.195 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2447 ; 0.232 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1951 ; 0.190 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1515 ; 0.112 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 308 ; 0.146 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.092 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.246 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 43 ; 0.249 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 30 ; 0.198 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.231 ; 0.200 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): 2000 ; 0.673 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 787 ; 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3323 ; 1.182 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2158 ; 1.551 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2479 ; 2.161 ; 4.500 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 : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C -4 C 0 REMARK 3 RESIDUE RANGE : D -4 D 0 REMARK 3 RESIDUE RANGE : E 1 E 4 REMARK 3 RESIDUE RANGE : F 1 F 4 REMARK 3 ORIGIN FOR THE GROUP (A): 0.1730 15.7170 83.1890 REMARK 3 T TENSOR REMARK 3 T11: -0.0679 T22: 0.0188 REMARK 3 T33: -0.0433 T12: -0.0033 REMARK 3 T13: -0.0055 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 1.0449 L22: 0.8138 REMARK 3 L33: 1.3520 L12: 0.0039 REMARK 3 L13: 0.4825 L23: 0.0305 REMARK 3 S TENSOR REMARK 3 S11: 0.0107 S12: -0.0147 S13: -0.0078 REMARK 3 S21: -0.0016 S22: 0.0134 S23: 0.0248 REMARK 3 S31: 0.0731 S32: 0.0294 S33: -0.0241 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -9 A 127 REMARK 3 RESIDUE RANGE : B 143 B 170 REMARK 3 ORIGIN FOR THE GROUP (A): -0.3750 11.9790 98.7660 REMARK 3 T TENSOR REMARK 3 T11: -0.0973 T22: 0.0532 REMARK 3 T33: -0.0558 T12: -0.0059 REMARK 3 T13: -0.0156 T23: 0.0128 REMARK 3 L TENSOR REMARK 3 L11: 1.0129 L22: 0.8648 REMARK 3 L33: 1.7726 L12: -0.2085 REMARK 3 L13: 0.4526 L23: -0.2341 REMARK 3 S TENSOR REMARK 3 S11: 0.0317 S12: -0.2067 S13: -0.0470 REMARK 3 S21: -0.0148 S22: 0.0839 S23: 0.0921 REMARK 3 S31: 0.1240 S32: -0.1568 S33: -0.1156 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -9 B 127 REMARK 3 RESIDUE RANGE : A 143 A 170 REMARK 3 ORIGIN FOR THE GROUP (A): 0.5690 11.0060 67.8270 REMARK 3 T TENSOR REMARK 3 T11: -0.0901 T22: 0.0464 REMARK 3 T33: -0.0652 T12: 0.0056 REMARK 3 T13: -0.0302 T23: -0.0220 REMARK 3 L TENSOR REMARK 3 L11: 1.0443 L22: 0.8621 REMARK 3 L33: 1.6468 L12: 0.0601 REMARK 3 L13: 0.4530 L23: 0.4661 REMARK 3 S TENSOR REMARK 3 S11: 0.0602 S12: 0.1867 S13: -0.0426 REMARK 3 S21: 0.0343 S22: 0.0523 S23: -0.0239 REMARK 3 S31: 0.0997 S32: 0.1467 S33: -0.1126 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 128 A 142 REMARK 3 RESIDUE RANGE : B 128 B 142 REMARK 3 ORIGIN FOR THE GROUP (A): -0.2890 -7.7250 83.8890 REMARK 3 T TENSOR REMARK 3 T11: 0.2733 T22: -0.1516 REMARK 3 T33: 0.0359 T12: -0.0139 REMARK 3 T13: -0.1656 T23: 0.0201 REMARK 3 L TENSOR REMARK 3 L11: 2.8549 L22: 2.0291 REMARK 3 L33: 7.0090 L12: -0.4284 REMARK 3 L13: 0.0382 L23: 0.9342 REMARK 3 S TENSOR REMARK 3 S11: 0.1069 S12: -0.0272 S13: -0.6238 REMARK 3 S21: 0.0900 S22: 0.1799 S23: 0.1034 REMARK 3 S31: 1.3767 S32: -0.0146 S33: -0.2868 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ACCORDING TO THE MS DATA, THE REMARK 3 SELENOMETHIONINE SUBSTITUTION WAS SUCCESSFUL ONLY IN PART. REMARK 3 THEREFORE, ONLY MET56 WAS MODELED AS SELENOMETHIONINE. HOWEVER, REMARK 3 ALL THREE MET POSITIONS ARE LIKELY TO BE PARTIALLY OCCUPIED BY REMARK 3 MET AND PARTIALLY BY MSE.THE CNS PROGRAM HAS BEEN USED FOR DNA REMARK 3 REFINEMENT. NO SUGAR PUCKER CONSTRAINTS HAVE BEEN APPLIED. REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REMARK 3 REFINEMENT HAS BEEN USED. REMARK 4 REMARK 4 3OR3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000061467. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MPG/DESY, HAMBURG REMARK 200 BEAMLINE : BW6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.281 REMARK 200 MONOCHROMATOR : TRIANGULAR MONOCHROMATOR REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35348 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 13.99 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 37.7750 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 14.78 REMARK 200 R MERGE FOR SHELL (I) : 0.40600 REMARK 200 R SYM FOR SHELL (I) : 0.40600 REMARK 200 FOR SHELL : 6.488 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: ARP/WARP REMARK 200 STARTING MODEL: 3OQG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES/NAOH PH 6.2 AND 30% MPD. REMARK 280 CRYSTAL WAS SOAKED IN 0.1 M CACL2 FOR 18 H., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 110.89150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.69750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.69750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.44575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.69750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.69750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 166.33725 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.69750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.69750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.44575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.69750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.69750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 166.33725 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 110.89150 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOLOGICAL UNIT CONTAINS PROTEIN CHAINS A AND B, DNA STRANDS C/E REMARK 300 (DNA STRAND T CLEAVED) AND DNA STRANDS D/E (DNA STRAND A CLEAVED) REMARK 300 . THE HEXAMER (ACCORDING TO THE PDB CONVENTIONS) IS A COMPLEX OF REMARK 300 THE DIMERIC RESTRICTION ENZYME WITH ITS PRODUCTS, TWO DOUBLE REMARK 300 STRANDED DNA FRAGMENTS. THE NATURAL PROTEIN OLIGOMERIZATION REMARK 300 STATE IS A DIMER - THE DNA IS A PRODUCT. UNDER THE PHYSIOLOGICAL REMARK 300 CONDITIONS THE PROTEIN DIMER BINDS DOUBLE STRANDED DNA AND REMARK 300 CLEAVES IT TO TWO DOUBLE STRANDED DNA FRAGMENTS. 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -139.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 222 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 260 LIES ON A SPECIAL POSITION. 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 MET A -9 REMARK 465 GLY A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 MET B -9 REMARK 465 GLY B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 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 DG E 1 P DG E 1 OP3 -0.091 REMARK 500 DG E 1 P DG E 1 OP3 -0.097 REMARK 500 DG F 1 P DG F 1 OP3 -0.095 REMARK 500 DG F 1 P DG F 1 OP3 -0.099 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 ASN B 161 10.58 81.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DT C -2 0.08 SIDE CHAIN REMARK 500 DT D -2 0.07 SIDE CHAIN REMARK 500 DG E 1 0.06 SIDE CHAIN REMARK 500 DG F 1 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 171, CONFORMER A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 172, CONFORMER A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 173 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 174 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 175, CONFORMER A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 171 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 171, CONFORMER B REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 172, CONFORMER B REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 175, CONFORMER B REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 176 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OQG RELATED DB: PDB REMARK 900 RESTRICTION ENDONUCLEASE HPY188I IN COMPLEX WITH SUBSTRATE DNA REMARK 900 RELATED ID: 3MX1 RELATED DB: PDB REMARK 900 THE STRUCTURE OF GIY-YIG ENDONUCLEASE R.ECO29KI REMARK 900 RELATED ID: 3MX4 RELATED DB: PDB REMARK 900 DNA BINDING AND CLEAVAGE BY THE GIY-YIG ENDONUCLEASE R.ECO29KI REMARK 900 INACTIVE VARIANT E142Q REMARK 900 RELATED ID: 3NIC RELATED DB: PDB REMARK 900 DNA BINDING AND CLEAVAGE BY THE GIY-YIG ENDONUCLEASE R.ECO29KI REMARK 900 INACTIVE VARIANT Y49F REMARK 900 RELATED ID: 2WSH RELATED DB: PDB REMARK 900 STRUCTURE OF BACTERIOPHAGE T4 ENDOII E118A MUTANT REMARK 900 RELATED ID: 1MK0 RELATED DB: PDB REMARK 900 CATALYTIC DOMAIN OF INTRON ENDONUCLEASE I-TEVI, E75A MUTANT REMARK 900 RELATED ID: 1YD1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE GIY-YIG N-TERMINAL ENDONUCLEASE DOMAIN OF REMARK 900 UVRC FROM THERMOTOGA MARITIMA BOUND TO ITS CATALYTIC DIVALENT REMARK 900 CATION: MAGNESIUM DBREF 3OR3 A 1 170 UNP Q9KJ88 Q9KJ88_HELPY 1 170 DBREF 3OR3 B 1 170 UNP Q9KJ88 Q9KJ88_HELPY 1 170 DBREF 3OR3 C -4 0 PDB 3OR3 3OR3 -4 0 DBREF 3OR3 D -4 0 PDB 3OR3 3OR3 -4 0 DBREF 3OR3 E 1 4 PDB 3OR3 3OR3 1 4 DBREF 3OR3 F 1 4 PDB 3OR3 3OR3 1 4 SEQADV 3OR3 MET A -9 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 GLY A -8 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 HIS A -7 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 HIS A -6 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 HIS A -5 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 HIS A -4 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 HIS A -3 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 HIS A -2 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 GLU A -1 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 PHE A 0 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 MET B -9 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 GLY B -8 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 HIS B -7 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 HIS B -6 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 HIS B -5 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 HIS B -4 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 HIS B -3 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 HIS B -2 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 GLU B -1 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OR3 PHE B 0 UNP Q9KJ88 EXPRESSION TAG SEQRES 1 A 180 MET GLY HIS HIS HIS HIS HIS HIS GLU PHE MET ALA LYS SEQRES 2 A 180 ARG LYS SER ASP ILE ILE LEU LYS SER VAL ASP ASP LEU SEQRES 3 A 180 LYS ASP GLU ILE ASP TYR LYS ASP PHE GLU TYR LYS GLU SEQRES 4 A 180 TYR PHE ASN LEU LEU CYS GLU LEU VAL PRO ASN ASN SER SEQRES 5 A 180 LEU GLU LYS LEU GLU ILE ASN ALA ILE ASP GLU LYS ASN SEQRES 6 A 180 MSE LYS ASN GLU GLY LEU VAL TYR VAL PHE VAL ILE GLN SEQRES 7 A 180 GLY LYS ILE PHE LYS ILE GLY HIS SER ILE THR PRO ILE SEQRES 8 A 180 THR LYS ARG VAL GLN SER TYR ASN CYS GLY LYS VAL GLU SEQRES 9 A 180 TYR ARG LYS ASN GLY THR CYS SER THR THR ASN TYR PHE SEQRES 10 A 180 VAL LEU GLN SER LEU LEU LYS ILE ASN LYS ILE VAL GLN SEQRES 11 A 180 VAL TYR ALA PHE PHE PRO GLU GLN PRO THR TYR THR LEU SEQRES 12 A 180 PHE GLY LYS THR TYR GLN ASP SER PHE SER THR SER LYS SEQRES 13 A 180 ARG ALA GLU ASN VAL ILE LEU GLU ASN PHE ILE LYS ASN SEQRES 14 A 180 HIS ASN LYS LYS PRO ILE GLY CYS THR GLN THR SEQRES 1 B 180 MET GLY HIS HIS HIS HIS HIS HIS GLU PHE MET ALA LYS SEQRES 2 B 180 ARG LYS SER ASP ILE ILE LEU LYS SER VAL ASP ASP LEU SEQRES 3 B 180 LYS ASP GLU ILE ASP TYR LYS ASP PHE GLU TYR LYS GLU SEQRES 4 B 180 TYR PHE ASN LEU LEU CYS GLU LEU VAL PRO ASN ASN SER SEQRES 5 B 180 LEU GLU LYS LEU GLU ILE ASN ALA ILE ASP GLU LYS ASN SEQRES 6 B 180 MSE LYS ASN GLU GLY LEU VAL TYR VAL PHE VAL ILE GLN SEQRES 7 B 180 GLY LYS ILE PHE LYS ILE GLY HIS SER ILE THR PRO ILE SEQRES 8 B 180 THR LYS ARG VAL GLN SER TYR ASN CYS GLY LYS VAL GLU SEQRES 9 B 180 TYR ARG LYS ASN GLY THR CYS SER THR THR ASN TYR PHE SEQRES 10 B 180 VAL LEU GLN SER LEU LEU LYS ILE ASN LYS ILE VAL GLN SEQRES 11 B 180 VAL TYR ALA PHE PHE PRO GLU GLN PRO THR TYR THR LEU SEQRES 12 B 180 PHE GLY LYS THR TYR GLN ASP SER PHE SER THR SER LYS SEQRES 13 B 180 ARG ALA GLU ASN VAL ILE LEU GLU ASN PHE ILE LYS ASN SEQRES 14 B 180 HIS ASN LYS LYS PRO ILE GLY CYS THR GLN THR SEQRES 1 C 5 DG DA DT DC DT SEQRES 1 D 5 DG DT DT DC DA SEQRES 1 E 4 DG DA DA DC SEQRES 1 F 4 DG DA DT DC MODRES 3OR3 MSE A 56 MET SELENOMETHIONINE MODRES 3OR3 MSE B 56 MET SELENOMETHIONINE HET MSE A 56 8 HET MSE B 56 8 HET CA A 171 1 HET CA A 172 1 HET CA A 173 1 HET CL A 174 1 HET CL A 175 2 HET CL A 176 1 HET CL B 171 1 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 7 CA 3(CA 2+) FORMUL 10 CL 4(CL 1-) FORMUL 14 HOH *311(H2 O) HELIX 1 1 ARG A 4 ILE A 8 5 5 HELIX 2 2 SER A 12 LYS A 17 5 6 HELIX 3 3 ASP A 21 PHE A 25 5 5 HELIX 4 4 TYR A 27 PHE A 31 5 5 HELIX 5 5 ASP A 52 MSE A 56 5 5 HELIX 6 6 PRO A 80 ASN A 89 1 10 HELIX 7 7 LYS A 92 GLY A 99 1 8 HELIX 8 8 SER A 102 ASN A 116 1 15 HELIX 9 9 SER A 143 ASN A 161 1 19 HELIX 10 10 ARG B 4 ILE B 8 5 5 HELIX 11 11 SER B 12 LYS B 17 5 6 HELIX 12 12 ASP B 21 PHE B 25 5 5 HELIX 13 13 TYR B 27 PHE B 31 5 5 HELIX 14 14 ASP B 52 MSE B 56 5 5 HELIX 15 15 PRO B 80 ASN B 89 1 10 HELIX 16 16 LYS B 92 GLY B 99 1 8 HELIX 17 17 SER B 102 ASN B 116 1 15 HELIX 18 18 SER B 143 ASN B 161 1 19 SHEET 1 A 5 LYS A 45 ALA A 50 0 SHEET 2 A 5 ASN A 32 ASN A 40 -1 N VAL A 38 O GLU A 47 SHEET 3 A 5 VAL A 119 PHE A 124 -1 O VAL A 121 N LEU A 34 SHEET 4 A 5 LEU A 61 ILE A 67 -1 N VAL A 66 O GLN A 120 SHEET 5 A 5 LYS A 70 SER A 77 -1 O LYS A 73 N PHE A 65 SHEET 1 B 2 TYR A 131 LEU A 133 0 SHEET 2 B 2 LYS A 136 TYR A 138 -1 O TYR A 138 N TYR A 131 SHEET 1 C 5 LYS B 45 ALA B 50 0 SHEET 2 C 5 ASN B 32 ASN B 40 -1 N VAL B 38 O GLU B 47 SHEET 3 C 5 VAL B 119 PHE B 124 -1 O VAL B 121 N CYS B 35 SHEET 4 C 5 LEU B 61 ILE B 67 -1 N VAL B 66 O GLN B 120 SHEET 5 C 5 LYS B 70 SER B 77 -1 O LYS B 73 N PHE B 65 SHEET 1 D 2 THR B 130 LEU B 133 0 SHEET 2 D 2 LYS B 136 GLN B 139 -1 O TYR B 138 N TYR B 131 LINK C ASN A 55 N MSE A 56 1555 1555 1.33 LINK C MSE A 56 N LYS A 57 1555 1555 1.33 LINK C ASN B 55 N MSE B 56 1555 1555 1.33 LINK C MSE B 56 N LYS B 57 1555 1555 1.34 SITE 1 AC1 6 GLU A 149 HIS B 76 DA D 0 DG F 1 SITE 2 AC1 6 HOH D 53 HOH F 39 SITE 1 AC2 6 GLU B 149 HIS A 76 DT C 0 DG E 1 SITE 2 AC2 6 HOH C 358 HOH F 52 SITE 1 AC3 6 ASP A 18 ASP B 18 HOH A 218 HOH A 219 SITE 2 AC3 6 HOH A 221 HOH A 222 SITE 1 AC4 4 ASN A 159 HIS A 160 GLU B 26 HOH A 210 SITE 1 AC5 4 SER B 143 HOH B 201 HOH B 230 HOH A 178 SITE 1 AC7 4 GLU A 26 ASN B 159 HIS B 160 HOH B 176 SITE 1 BC1 6 GLU A 149 HIS B 76 DT C 0 DG E 1 SITE 2 BC1 6 HOH D 53 HOH F 39 SITE 1 BC2 6 GLU B 149 HIS A 76 DA D 0 DG F 1 SITE 2 BC2 6 HOH C 358 HOH F 52 SITE 1 BC5 4 SER A 143 HOH A 276 HOH E 183 HOH B 181 SITE 1 BC6 2 LYS A 92 HOH D 323 CRYST1 65.395 65.395 221.783 90.00 90.00 90.00 P 41 21 2 16 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 0.015292 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015292 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004509 0.00000 MASTER 492 0 9 18 14 0 15 6 0 0 0 32 END