HEADER HYDROLASE/DNA 12-DEC-07 3BM3 TITLE RESTRICTION ENDONUCLEASE PSPGI-SUBSTRATE DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*AP*TP*CP*CP*AP*GP*GP*TP*AP*C)-3'); COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*GP*GP*AP*T)-3'); COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PSPGI RESTRICTION ENDONUCLEASE; COMPND 11 CHAIN: A, B; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: PYROCOCCUS SP. GI-H; SOURCE 7 ORGANISM_TAXID: 83521; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS ENDONUCLEASE-DNA COMPLEX, RESTRICTION ENZYME, PSPGI, BASE FLIPPING, KEYWDS 2 HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.H.SZCZEPANOWSKI,M.CARPENTER,H.CZAPINSKA,G.TAMULAITIS,V.SIKSNYS, AUTHOR 2 A.BHAGWAT,M.BOCHTLER REVDAT 5 20-OCT-21 3BM3 1 REMARK SEQADV LINK REVDAT 4 25-OCT-17 3BM3 1 REMARK REVDAT 3 13-JUL-11 3BM3 1 VERSN REVDAT 2 24-FEB-09 3BM3 1 VERSN REVDAT 1 16-SEP-08 3BM3 0 JRNL AUTH R.H.SZCZEPANOWSKI,M.CARPENTER,H.CZAPINSKA,G.TAMULAITIS, JRNL AUTH 2 V.SIKSNYS,A.BHAGWAT,M.BOCHTLER JRNL TITL A DIRECT CRYSTALLOGRAPHIC DEMONSTRATION THAT TYPE II JRNL TITL 2 RESTRICTION ENDONUCLEASE PSPGI FLIPS NUCLEOTIDES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.TAMULAITIS,M.ZAREMBA,R.H.SZCZEPANOWSKI,M.BOCHTLER, REMARK 1 AUTH 2 V.SIKSNYS REMARK 1 TITL NUCLEOTIDE FLIPPING BY RESTRICTION ENZYMES ANALYZED BY REMARK 1 TITL 2 2-AMINOPURINE STEADY-STATE FLUORESCENCE. REMARK 1 REF NUCLEIC ACIDS RES. V. 35 4792 2007 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 17617640 REMARK 1 DOI 10.1093/NAR/GKM513 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.CARPENTER,P.DIVVELA,V.PINGOUD,J.BUJNICKI,A.S.BHAGWAT REMARK 1 TITL SEQUENCE-DEPENDENT ENHANCEMENT OF HYDROLYTIC DEAMINATION OF REMARK 1 TITL 2 CYTOSINES IN DNA BY THE RESTRICTION ENZYME PSPGI. REMARK 1 REF NUCLEIC ACIDS RES. V. 34 3762 2006 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 16893959 REMARK 1 DOI 10.1093/NAR/GKL545 REMARK 1 REFERENCE 3 REMARK 1 AUTH V.PINGOUD,C.CONZELMANN,S.KINZEBACH,A.SUDINA,V.METELEV, REMARK 1 AUTH 2 E.KUBAREVA,J.M.BUJNICKI,R.LURZ,G.LUDER,S.Y.XU,A.PINGOUD REMARK 1 TITL PSPGI, A TYPE II RESTRICTION ENDONUCLEASE FROM THE EXTREME REMARK 1 TITL 2 THERMOPHILE PYROCOCCUS SP.: STRUCTURAL AND FUNCTIONAL REMARK 1 TITL 3 STUDIES TO INVESTIGATE AN EVOLUTIONARY RELATIONSHIP WITH REMARK 1 TITL 4 SEVERAL MESOPHILIC RESTRICTION ENZYMES. REMARK 1 REF J.MOL.BIOL. V. 329 913 2003 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 12798682 REMARK 1 DOI 10.1016/S0022-2836(03)00523-0 REMARK 1 REFERENCE 4 REMARK 1 AUTH R.MORGAN,J.XIAO,S.XU REMARK 1 TITL CHARACTERIZATION OF AN EXTREMELY THERMOSTABLE RESTRICTION REMARK 1 TITL 2 ENZYME, PSPGI, FROM A PYROCOCCUS STRAIN AND CLONING OF THE REMARK 1 TITL 3 PSPGI RESTRICTION-MODIFICATION SYSTEM IN ESCHERICHIA COLI. REMARK 1 REF APPL.ENVIRON.MICROBIOL. V. 64 3669 1998 REMARK 1 REFN ISSN 0099-2240 REMARK 1 PMID 9758783 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 63135 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3230 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4290 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE SET COUNT : 236 REMARK 3 BIN FREE R VALUE : 0.2220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4319 REMARK 3 NUCLEIC ACID ATOMS : 445 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 293 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 20.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.63000 REMARK 3 B22 (A**2) : -1.11000 REMARK 3 B33 (A**2) : 1.74000 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): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.099 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 : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5167 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3538 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7083 ; 1.369 ; 2.077 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8607 ; 3.852 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 567 ; 5.086 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 251 ;33.037 ;24.024 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 898 ;13.786 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;18.083 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 754 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5511 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1058 ; 0.010 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1308 ; 0.222 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4044 ; 0.252 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2669 ; 0.199 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2557 ; 0.103 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 361 ; 0.149 ; 0.200 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): 33 ; 0.223 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 70 ; 0.257 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.138 ; 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): 2739 ; 0.785 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1092 ; 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4496 ; 1.417 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2428 ; 2.344 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2587 ; 3.686 ; 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 : 5 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 : A 2 A 116 REMARK 3 ORIGIN FOR THE GROUP (A): 10.6200 44.3010 26.5350 REMARK 3 T TENSOR REMARK 3 T11: -0.0230 T22: -0.0076 REMARK 3 T33: -0.0264 T12: -0.0221 REMARK 3 T13: 0.0210 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 0.3369 L22: 2.6192 REMARK 3 L33: 0.6845 L12: 0.1164 REMARK 3 L13: 0.1181 L23: 1.1657 REMARK 3 S TENSOR REMARK 3 S11: 0.0236 S12: -0.1015 S13: -0.0025 REMARK 3 S21: 0.1321 S22: -0.0748 S23: 0.1623 REMARK 3 S31: 0.1026 S32: -0.0326 S33: 0.0512 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 117 A 260 REMARK 3 ORIGIN FOR THE GROUP (A): 25.1460 64.2380 21.3420 REMARK 3 T TENSOR REMARK 3 T11: -0.0079 T22: -0.0378 REMARK 3 T33: -0.0130 T12: -0.0078 REMARK 3 T13: 0.0011 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 0.8230 L22: 0.1630 REMARK 3 L33: 0.8565 L12: -0.0817 REMARK 3 L13: -0.2744 L23: -0.1408 REMARK 3 S TENSOR REMARK 3 S11: 0.0373 S12: -0.0706 S13: 0.1169 REMARK 3 S21: -0.0013 S22: -0.0098 S23: 0.0106 REMARK 3 S31: -0.0463 S32: 0.0266 S33: -0.0275 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 : B 3 B 116 REMARK 3 ORIGIN FOR THE GROUP (A): 36.1480 31.1280 5.7150 REMARK 3 T TENSOR REMARK 3 T11: 0.0233 T22: -0.0263 REMARK 3 T33: -0.0209 T12: 0.0115 REMARK 3 T13: 0.0194 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.1689 L22: 0.5480 REMARK 3 L33: 0.7019 L12: 0.2793 REMARK 3 L13: -0.2922 L23: -0.4117 REMARK 3 S TENSOR REMARK 3 S11: -0.0153 S12: -0.0120 S13: -0.0669 REMARK 3 S21: -0.0547 S22: 0.0478 S23: -0.0648 REMARK 3 S31: 0.0694 S32: 0.0104 S33: -0.0325 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 117 B 260 REMARK 3 ORIGIN FOR THE GROUP (A): 37.2970 55.8660 1.2650 REMARK 3 T TENSOR REMARK 3 T11: -0.0018 T22: -0.0262 REMARK 3 T33: -0.0228 T12: -0.0205 REMARK 3 T13: 0.0139 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 0.4988 L22: 0.5720 REMARK 3 L33: 0.7173 L12: -0.1151 REMARK 3 L13: -0.0434 L23: 0.2778 REMARK 3 S TENSOR REMARK 3 S11: -0.0143 S12: 0.0350 S13: 0.0697 REMARK 3 S21: -0.0598 S22: 0.0386 S23: -0.0603 REMARK 3 S31: -0.0236 S32: 0.0405 S33: -0.0243 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C -5 C 5 REMARK 3 RESIDUE RANGE : D -6 D 4 REMARK 3 ORIGIN FOR THE GROUP (A): 26.4000 43.8350 14.7650 REMARK 3 T TENSOR REMARK 3 T11: 0.0051 T22: -0.0158 REMARK 3 T33: -0.0179 T12: -0.0024 REMARK 3 T13: 0.0033 T23: -0.0006 REMARK 3 L TENSOR REMARK 3 L11: 0.5332 L22: 0.7940 REMARK 3 L33: 0.4988 L12: -0.2184 REMARK 3 L13: -0.4552 L23: 0.0142 REMARK 3 S TENSOR REMARK 3 S11: -0.0244 S12: -0.0162 S13: 0.0421 REMARK 3 S21: 0.0162 S22: 0.0122 S23: -0.0509 REMARK 3 S31: 0.0201 S32: 0.0364 S33: 0.0122 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: CNS HAS BEEN USED FOR DNA REFINEMENT. REMARK 3 NO CONSTRAINTS FOR SUGAR PUCKER WERE APPLIED. RESIDUES AT THE REMARK 3 ENDS OF THE DNA DUPLEX ( 5 AND 5 IN CHAIN C AND -6 AND -5 IN REMARK 3 CHAIN D) HAVE POOR DENSITY. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. TLS REFINEMENT HAS BEEN USED. REMARK 4 REMARK 4 3BM3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045686. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 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) : 0.976 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 : 63138 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 21.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25400 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHELXD, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% MPD, 0.1 M CITRIC ACID, 0.1 M REMARK 280 COBALT (II) CHLORIDE AS AN ADDITIVE, PH 4.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 294K 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 23.44200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.53450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.03000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.53450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.44200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.03000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE TETRAMER (ACCORDING TO PDB CONVENTIONS) IS A COMPLEX OF REMARK 300 THE DIMERIC RESTRICTION ENZYME WITH ITS SUBSTRATE, DOUBLE STRANDED REMARK 300 DNA. 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: 10070 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A, 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 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 MSE A 1 REMARK 465 GLY A 261 REMARK 465 ASN A 262 REMARK 465 LYS A 263 REMARK 465 LYS A 264 REMARK 465 ARG A 265 REMARK 465 GLY A 266 REMARK 465 LYS A 267 REMARK 465 GLN A 268 REMARK 465 LEU A 269 REMARK 465 THR A 270 REMARK 465 LEU A 271 REMARK 465 VAL A 272 REMARK 465 MSE B 1 REMARK 465 VAL B 2 REMARK 465 GLY B 261 REMARK 465 ASN B 262 REMARK 465 LYS B 263 REMARK 465 LYS B 264 REMARK 465 ARG B 265 REMARK 465 GLY B 266 REMARK 465 LYS B 267 REMARK 465 GLN B 268 REMARK 465 LEU B 269 REMARK 465 THR B 270 REMARK 465 LEU B 271 REMARK 465 VAL B 272 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG B 3 NE CZ NH1 NH2 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 ARG A 161 -107.10 -81.61 REMARK 500 ARG A 164 -133.35 46.13 REMARK 500 ARG B 161 -104.43 -84.48 REMARK 500 ARG B 164 -131.82 47.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT B 273 DBREF 3BM3 A 1 272 UNP O93646 O93646_9EURY 1 272 DBREF 3BM3 B 1 272 UNP O93646 O93646_9EURY 1 272 DBREF 3BM3 C -5 5 PDB 3BM3 3BM3 -5 5 DBREF 3BM3 D -6 4 PDB 3BM3 3BM3 -6 4 SEQADV 3BM3 ALA A 138 UNP O93646 ASP 138 ENGINEERED MUTATION SEQADV 3BM3 THR A 146 UNP O93646 ALA 146 ENGINEERED MUTATION SEQADV 3BM3 ALA B 138 UNP O93646 ASP 138 ENGINEERED MUTATION SEQADV 3BM3 THR B 146 UNP O93646 ALA 146 ENGINEERED MUTATION SEQRES 1 C 11 DC DA DT DC DC DA DG DG DT DA DC SEQRES 1 D 11 DG DG DT DA DC DC DT DG DG DA DT SEQRES 1 A 272 MSE VAL ARG ASN LEU VAL ILE ASP ILE THR LYS LYS PRO SEQRES 2 A 272 THR GLN ASN ILE PRO PRO THR ASN GLU ILE ILE GLU GLU SEQRES 3 A 272 ALA ILE THR GLU LEU ASN VAL ASP GLU LEU LEU ASP ARG SEQRES 4 A 272 LEU PHE GLU LYS ASP GLU SER GLY GLU VAL ILE THR PRO SEQRES 5 A 272 SER ARG ILE ALA LYS MSE LEU GLU GLU LYS ALA PHE GLU SEQRES 6 A 272 ILE TYR LYS GLU TYR GLU LYS GLN VAL ARG GLU ALA TYR SEQRES 7 A 272 LEU SER ALA GLY TYR SER ARG GLU LYS LEU GLU GLN SER SEQRES 8 A 272 PHE GLN GLN ALA ARG PHE SER ARG GLY GLY LYS ALA PHE SEQRES 9 A 272 GLU ILE ILE PHE THR LYS LEU LEU ASN LYS PHE GLY ILE SEQRES 10 A 272 ARG TYR GLU HIS ASP ARG VAL ILE LYS ILE TYR ASP TYR SEQRES 11 A 272 ILE THR GLU GLY GLU LYS PRO ALA PHE ILE ILE PRO SER SEQRES 12 A 272 VAL ARG THR PHE LEU ASN ASP PRO SER SER ALA ILE LEU SEQRES 13 A 272 ILE THR VAL LYS ARG LYS VAL ARG GLU ARG TRP ARG GLU SEQRES 14 A 272 ALA VAL GLY GLU ALA GLN ILE LEU ARG ASN LYS PHE GLY SEQRES 15 A 272 ASP GLU ILE ASN PHE TRP PHE VAL GLY PHE ASP GLU GLU SEQRES 16 A 272 PHE THR ILE TYR SER ALA ILE ALA MSE LEU ASP ASN GLY SEQRES 17 A 272 ILE ASP ARG VAL TYR VAL ILE ASP GLY ARG TYR ASP SER SEQRES 18 A 272 LEU ILE GLU GLU ILE LYS ARG ILE SER ASP PRO ASN PHE SEQRES 19 A 272 ASN GLU ASP LYS TYR ILE GLN LYS ILE ARG ARG PHE SER SEQRES 20 A 272 ASP ILE PHE ASP ASP ILE ILE GLN PHE LEU ASN LYS HIS SEQRES 21 A 272 GLY ASN LYS LYS ARG GLY LYS GLN LEU THR LEU VAL SEQRES 1 B 272 MSE VAL ARG ASN LEU VAL ILE ASP ILE THR LYS LYS PRO SEQRES 2 B 272 THR GLN ASN ILE PRO PRO THR ASN GLU ILE ILE GLU GLU SEQRES 3 B 272 ALA ILE THR GLU LEU ASN VAL ASP GLU LEU LEU ASP ARG SEQRES 4 B 272 LEU PHE GLU LYS ASP GLU SER GLY GLU VAL ILE THR PRO SEQRES 5 B 272 SER ARG ILE ALA LYS MSE LEU GLU GLU LYS ALA PHE GLU SEQRES 6 B 272 ILE TYR LYS GLU TYR GLU LYS GLN VAL ARG GLU ALA TYR SEQRES 7 B 272 LEU SER ALA GLY TYR SER ARG GLU LYS LEU GLU GLN SER SEQRES 8 B 272 PHE GLN GLN ALA ARG PHE SER ARG GLY GLY LYS ALA PHE SEQRES 9 B 272 GLU ILE ILE PHE THR LYS LEU LEU ASN LYS PHE GLY ILE SEQRES 10 B 272 ARG TYR GLU HIS ASP ARG VAL ILE LYS ILE TYR ASP TYR SEQRES 11 B 272 ILE THR GLU GLY GLU LYS PRO ALA PHE ILE ILE PRO SER SEQRES 12 B 272 VAL ARG THR PHE LEU ASN ASP PRO SER SER ALA ILE LEU SEQRES 13 B 272 ILE THR VAL LYS ARG LYS VAL ARG GLU ARG TRP ARG GLU SEQRES 14 B 272 ALA VAL GLY GLU ALA GLN ILE LEU ARG ASN LYS PHE GLY SEQRES 15 B 272 ASP GLU ILE ASN PHE TRP PHE VAL GLY PHE ASP GLU GLU SEQRES 16 B 272 PHE THR ILE TYR SER ALA ILE ALA MSE LEU ASP ASN GLY SEQRES 17 B 272 ILE ASP ARG VAL TYR VAL ILE ASP GLY ARG TYR ASP SER SEQRES 18 B 272 LEU ILE GLU GLU ILE LYS ARG ILE SER ASP PRO ASN PHE SEQRES 19 B 272 ASN GLU ASP LYS TYR ILE GLN LYS ILE ARG ARG PHE SER SEQRES 20 B 272 ASP ILE PHE ASP ASP ILE ILE GLN PHE LEU ASN LYS HIS SEQRES 21 B 272 GLY ASN LYS LYS ARG GLY LYS GLN LEU THR LEU VAL MODRES 3BM3 MSE A 58 MET SELENOMETHIONINE MODRES 3BM3 MSE A 204 MET SELENOMETHIONINE MODRES 3BM3 MSE B 58 MET SELENOMETHIONINE MODRES 3BM3 MSE B 204 MET SELENOMETHIONINE HET MSE A 58 16 HET MSE A 204 16 HET MSE B 58 16 HET MSE B 204 16 HET CIT B 273 13 HETNAM MSE SELENOMETHIONINE HETNAM CIT CITRIC ACID FORMUL 3 MSE 4(C5 H11 N O2 SE) FORMUL 5 CIT C6 H8 O7 FORMUL 6 HOH *293(H2 O) HELIX 1 1 LYS A 12 ILE A 17 5 6 HELIX 2 2 PRO A 19 ASN A 32 1 14 HELIX 3 3 ASN A 32 ARG A 39 1 8 HELIX 4 4 THR A 51 ALA A 81 1 31 HELIX 5 5 SER A 84 GLY A 116 1 33 HELIX 6 6 SER A 143 ASP A 150 1 8 HELIX 7 7 PRO A 151 SER A 153 5 3 HELIX 8 8 ARG A 166 GLY A 182 1 17 HELIX 9 9 THR A 197 ASN A 207 1 11 HELIX 10 10 ILE A 215 ARG A 228 1 14 HELIX 11 11 ASN A 235 GLN A 241 1 7 HELIX 12 12 ASP A 248 HIS A 260 1 13 HELIX 13 13 LYS B 12 ILE B 17 5 6 HELIX 14 14 PRO B 19 LEU B 31 1 13 HELIX 15 15 ASN B 32 ASP B 38 1 7 HELIX 16 16 THR B 51 ALA B 81 1 31 HELIX 17 17 SER B 84 PHE B 115 1 32 HELIX 18 18 SER B 143 ASP B 150 1 8 HELIX 19 19 PRO B 151 ALA B 154 5 4 HELIX 20 20 ARG B 166 GLY B 182 1 17 HELIX 21 21 THR B 197 ASP B 206 1 10 HELIX 22 22 ILE B 215 ARG B 228 1 14 HELIX 23 23 ASN B 235 LYS B 242 1 8 HELIX 24 24 ASP B 248 HIS B 260 1 13 SHEET 1 A 2 ILE A 125 LYS A 126 0 SHEET 2 A 2 GLY A 134 GLU A 135 -1 O GLU A 135 N ILE A 125 SHEET 1 B 5 PHE A 139 ILE A 141 0 SHEET 2 B 5 ILE A 155 LYS A 160 -1 O ILE A 155 N ILE A 141 SHEET 3 B 5 ASN A 186 GLY A 191 1 O TRP A 188 N LEU A 156 SHEET 4 B 5 ARG A 211 VAL A 214 1 O TYR A 213 N PHE A 189 SHEET 5 B 5 ILE A 243 ARG A 245 1 O ARG A 244 N VAL A 212 SHEET 1 C 6 GLU B 120 HIS B 121 0 SHEET 2 C 6 PHE B 139 ILE B 141 -1 O ILE B 140 N GLU B 120 SHEET 3 C 6 ILE B 155 VAL B 159 -1 O ILE B 155 N ILE B 141 SHEET 4 C 6 PHE B 187 VAL B 190 1 O TRP B 188 N LEU B 156 SHEET 5 C 6 ARG B 211 VAL B 214 1 O TYR B 213 N PHE B 189 SHEET 6 C 6 ILE B 243 ARG B 245 1 O ARG B 244 N VAL B 212 LINK C LYS A 57 N AMSE A 58 1555 1555 1.33 LINK C LYS A 57 N BMSE A 58 1555 1555 1.33 LINK C AMSE A 58 N LEU A 59 1555 1555 1.33 LINK C BMSE A 58 N LEU A 59 1555 1555 1.33 LINK C ALA A 203 N AMSE A 204 1555 1555 1.33 LINK C ALA A 203 N BMSE A 204 1555 1555 1.33 LINK C AMSE A 204 N LEU A 205 1555 1555 1.32 LINK C BMSE A 204 N LEU A 205 1555 1555 1.33 LINK C LYS B 57 N AMSE B 58 1555 1555 1.33 LINK C LYS B 57 N BMSE B 58 1555 1555 1.33 LINK C AMSE B 58 N LEU B 59 1555 1555 1.33 LINK C BMSE B 58 N LEU B 59 1555 1555 1.33 LINK C ALA B 203 N AMSE B 204 1555 1555 1.33 LINK C ALA B 203 N BMSE B 204 1555 1555 1.33 LINK C AMSE B 204 N LEU B 205 1555 1555 1.32 LINK C BMSE B 204 N LEU B 205 1555 1555 1.32 CISPEP 1 ILE A 141 PRO A 142 0 2.28 CISPEP 2 ILE B 141 PRO B 142 0 0.62 SITE 1 AC1 8 ASP B 210 ARG B 211 GLN B 241 LYS B 242 SITE 2 AC1 8 HOH B 289 HOH B 330 HOH B 334 HOH B 383 CRYST1 46.884 96.060 127.069 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 0.021329 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010410 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007870 0.00000