PDB Short entry for 3OQG 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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