HEADER HYDROLASE/DNA 03-SEP-10 3OQG TITLE RESTRICTION ENDONUCLEASE HPY188I IN COMPLEX WITH SUBSTRATE DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HPY188I; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA 5'-D(*GP*AP*TP*CP*TP*GP*AP*AP*C)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA 5'-D(*GP*TP*TP*CP*AP*GP*AP*TP*C)-3'; COMPND 11 CHAIN: D; COMPND 12 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; 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 KEYWDS ENDONUCLEASE-DNA COMPLEX, RESTRICTION ENZYME, HPY188I, INTERCALATION, KEYWDS 2 GIY-YIG NUCLEASE, CATALYTIC MECHANISM, PSEUDOPALINDROME, HYDROLASE- KEYWDS 3 DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.SOKOLOWSKA,H.CZAPINSKA,M.BOCHTLER REVDAT 4 08-NOV-17 3OQG 1 REMARK REVDAT 3 06-APR-11 3OQG 1 JRNL REVDAT 2 05-JAN-11 3OQG 1 JRNL REVDAT 1 20-OCT-10 3OQG 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. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 48287 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2393 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3222 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 216 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2894 REMARK 3 NUCLEIC ACID ATOMS : 363 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 359 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.70000 REMARK 3 B22 (A**2) : 0.70000 REMARK 3 B33 (A**2) : -1.40000 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): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4222 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2657 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5906 ; 1.224 ; 2.172 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6612 ; 3.961 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 445 ; 5.580 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 175 ;38.222 ;26.057 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 667 ;15.094 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;13.779 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 636 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4353 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 745 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 793 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2450 ; 0.230 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1960 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1536 ; 0.112 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 353 ; 0.151 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.156 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 8 ; 0.075 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 39 ; 0.208 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 46 ; 0.230 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.182 ; 0.200 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): 2036 ; 0.600 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 801 ; 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3387 ; 1.107 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2186 ; 1.492 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2514 ; 2.251 ; 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C -4 C 4 REMARK 3 RESIDUE RANGE : D -4 D 4 REMARK 3 ORIGIN FOR THE GROUP (A): 0.4550 15.7510 82.6630 REMARK 3 T TENSOR REMARK 3 T11: -0.0631 T22: 0.0048 REMARK 3 T33: -0.0250 T12: -0.0025 REMARK 3 T13: -0.0100 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 0.0917 L22: 1.0832 REMARK 3 L33: 1.1944 L12: 0.0192 REMARK 3 L13: 0.3307 L23: 0.0189 REMARK 3 S TENSOR REMARK 3 S11: 0.0103 S12: -0.0140 S13: -0.0083 REMARK 3 S21: -0.0347 S22: -0.0140 S23: 0.0090 REMARK 3 S31: 0.0626 S32: 0.0167 S33: 0.0038 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): -0.0680 12.0570 98.1700 REMARK 3 T TENSOR REMARK 3 T11: -0.0692 T22: 0.0341 REMARK 3 T33: -0.0381 T12: -0.0242 REMARK 3 T13: -0.0101 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 0.3773 L22: 0.8053 REMARK 3 L33: 1.4591 L12: -0.1890 REMARK 3 L13: 0.3769 L23: -0.2043 REMARK 3 S TENSOR REMARK 3 S11: 0.0357 S12: -0.0657 S13: 0.0044 REMARK 3 S21: 0.0035 S22: -0.0107 S23: 0.0894 REMARK 3 S31: 0.1067 S32: -0.1489 S33: -0.0250 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): 0.8600 10.9660 67.3900 REMARK 3 T TENSOR REMARK 3 T11: -0.0779 T22: 0.0461 REMARK 3 T33: -0.0601 T12: 0.0030 REMARK 3 T13: -0.0220 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 0.7700 L22: 0.8696 REMARK 3 L33: 1.2098 L12: 0.1204 REMARK 3 L13: 0.3822 L23: 0.3829 REMARK 3 S TENSOR REMARK 3 S11: 0.0339 S12: 0.1408 S13: -0.0048 REMARK 3 S21: 0.0154 S22: 0.0268 S23: -0.0387 REMARK 3 S31: 0.0346 S32: 0.1211 S33: -0.0607 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): 0.1590 -7.6240 83.4610 REMARK 3 T TENSOR REMARK 3 T11: 0.2383 T22: -0.1078 REMARK 3 T33: -0.0004 T12: -0.0031 REMARK 3 T13: -0.1090 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 4.2513 L22: 3.6681 REMARK 3 L33: 6.0910 L12: 0.0483 REMARK 3 L13: 1.1016 L23: 0.2765 REMARK 3 S TENSOR REMARK 3 S11: 0.0779 S12: 0.0026 S13: -0.4532 REMARK 3 S21: 0.0911 S22: 0.0771 S23: 0.0203 REMARK 3 S31: 1.0411 S32: 0.0084 S33: -0.1550 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: REMARK 3 THE DENSITY FOR THE NUCLEOPHILIC WATER MOLECULES (RESIDUES A173 & REMARK 3 B172) IS VERY WEAK. IT MIGHT CORRESPOND TO A (HALF OCCUPIED) WATER REMARK 3 MOLECULE OR A HYDROXIDE ION. REMARK 3 ACCORDING TO THE MS DATA, THE SELENOMETHIONINE SUBSTITUTION WAS REMARK 3 SUCCESSFUL ONLY IN PART. THEREFORE, ONLY MET56 WAS MODELED AS REMARK 3 SELENOMETHIONINE. HOWEVER, ALL THREE MET POSITIONS ARE LIKELY TO REMARK 3 BE PARTIALLY OCCUPIED BY MET AND PARTIALLY BY MSE.THE CNS PROGRAM REMARK 3 HAS BEEN USED FOR DNA REFINEMENT. REMARK 3 NO SUGAR PUCKER CONSTRAINTS HAVE BEEN APPLIED. HYDROGENS HAVE BEEN REMARK 3 ADDED IN THE RIDING POSITIONS. REMARK 3 TLS REFINEMENT HAS BEEN USED. REMARK 4 REMARK 4 3OQG 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_1000061444. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-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) : 1.05 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 : 48330 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5.550 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 24.6510 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.55 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : 0.44000 REMARK 200 FOR SHELL : 3.265 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXCD, SHELXD, MLPHARE, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES/NAOH PH 6.2 AND 30% MPD, REMARK 280 VAPOR DIFFUSION, 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 110.31500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.61800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.61800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.15750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.61800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.61800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 165.47250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.61800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.61800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.15750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.61800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.61800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 165.47250 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 110.31500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOLOGICAL UNIT CONTAINS PROTEIN CHAINS A AND B, DNA STRANDS C REMARK 300 AND D. THE TETRAMER (ACCORDING TO PDB CONVENTIONS) IS A COMPLEX REMARK 300 OF THE DIMERIC RESTRICTION ENZYME WITH ITS SUBSTRATE, DOUBLE REMARK 300 STRANDED DNA. THE NATURAL PROTEIN OLIGOMERIZATION STATE IS A REMARK 300 DIMER - THE DNA IS A SUBSTRATE. 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -9 REMARK 465 GLY A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 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 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 D 1 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 DG D 1 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DG D 1 O4' - C1' - N9 ANGL. DEV. = 2.1 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 THR A 168 -50.99 -121.75 REMARK 500 THR B 168 -51.46 -124.74 REMARK 500 THR B 168 -52.88 -124.74 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 NA A 171, CONFORMER A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 172 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 171, CONFORMER A REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 171, CONFORMER B REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 171, CONFORMER B REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OR3 RELATED DB: PDB REMARK 900 RESTRICTION ENDONUCLEASE HPY188I IN COMPLEX WITH PRODUCT 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 3OQG A 1 170 UNP Q9KJ88 Q9KJ88_HELPY 1 170 DBREF 3OQG B 1 170 UNP Q9KJ88 Q9KJ88_HELPY 1 170 DBREF 3OQG C -4 4 PDB 3OQG 3OQG -4 4 DBREF 3OQG D -4 4 PDB 3OQG 3OQG -4 4 SEQADV 3OQG MET A -9 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG GLY A -8 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG HIS A -7 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG HIS A -6 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG HIS A -5 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG HIS A -4 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG HIS A -3 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG HIS A -2 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG GLU A -1 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG PHE A 0 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG MET B -9 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG GLY B -8 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG HIS B -7 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG HIS B -6 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG HIS B -5 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG HIS B -4 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG HIS B -3 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG HIS B -2 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG GLU B -1 UNP Q9KJ88 EXPRESSION TAG SEQADV 3OQG 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 9 DG DA DT DC DT DG DA DA DC SEQRES 1 D 9 DG DT DT DC DA DG DA DT DC MODRES 3OQG MSE A 56 MET SELENOMETHIONINE MODRES 3OQG MSE B 56 MET SELENOMETHIONINE HET MSE A 56 8 HET MSE B 56 8 HET NA A 171 1 HET CL A 172 1 HET NA B 171 1 HETNAM MSE SELENOMETHIONINE HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 5 NA 2(NA 1+) FORMUL 6 CL CL 1- FORMUL 8 HOH *359(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 GLU A 36 O ASN A 49 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 PHE A 72 N PHE A 65 SHEET 1 B 2 THR A 130 LEU A 133 0 SHEET 2 B 2 LYS A 136 GLN A 139 -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 GLU B 36 O ASN B 49 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 PHE B 72 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 1.32 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 HOH A 238 HOH A 276 HOH B 203 SITE 2 AC1 6 DA D 0 DG D 1 SITE 1 AC2 4 ASN A 159 HIS A 160 HOH A 307 GLU B 26 SITE 1 AC3 6 GLU B 149 HOH A 218 HOH B 216 HOH B 232 SITE 2 AC3 6 DT C 0 DG C 1 SITE 1 BC1 6 GLU A 149 HOH A 238 HOH A 276 HOH B 203 SITE 2 BC1 6 DT C 0 DG C 1 SITE 1 BC3 6 GLU B 149 HOH A 218 HOH B 216 HOH B 232 SITE 2 BC3 6 DA D 0 DG D 1 CRYST1 65.236 65.236 220.630 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 0.015329 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015329 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004532 0.00000 MASTER 440 0 5 18 14 0 9 6 0 0 0 30 END