HEADER HYDROLASE 13-FEB-04 1SDO TITLE CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BSTYI COMPND MOL_ID: 1; COMPND 2 MOLECULE: BSTYI; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.21.4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: BSTYIR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ER2744 KEYWDS RESTRICTION ENDONUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.A.TOWNSON,J.C.SAMUELSON,E.S.VANAMEE,T.A.EDWARDS,C.R.ESCALANTE, AUTHOR 2 S.Y.XU,A.K.AGGARWAL REVDAT 3 14-FEB-24 1SDO 1 REMARK REVDAT 2 24-FEB-09 1SDO 1 VERSN REVDAT 1 11-MAY-04 1SDO 0 JRNL AUTH S.A.TOWNSON,J.C.SAMUELSON,E.S.VANAMEE,T.A.EDWARDS, JRNL AUTH 2 C.R.ESCALANTE,S.Y.XU,A.K.AGGARWAL JRNL TITL CRYSTAL STRUCTURE OF BSTYI AT 1.85 A RESOLUTION: A JRNL TITL 2 THERMOPHILIC RESTRICTION ENDONUCLEASE WITH OVERLAPPING JRNL TITL 3 SPECIFICITIES TO BAMHI AND BGLII JRNL REF J.MOL.BIOL. V. 338 725 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15099740 JRNL DOI 10.1016/J.JMB.2004.02.074 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 33604 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 SET) : 0.220 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3273 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1547 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 90 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.91500 REMARK 3 B22 (A**2) : -7.14800 REMARK 3 B33 (A**2) : 5.23000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.10 REMARK 3 LOW RESOLUTION CUTOFF (A) : 1.85 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : 1.291 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.93 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.829 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SDO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021620. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.973, 0.9282 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33604 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG-400, 0.1M HEPES, 200MM CALCIUM REMARK 280 CHLORIDE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.94500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.30500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.48500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.94500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.30500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.48500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.94500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.30500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.48500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.94500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.30500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 39.48500 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: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF A MONOMER (1 CHAIN). THE BIOLOGICAL DIMER IS REMARK 300 GENERATED BY THE OPERATIONS: ROTATION MATRIX -1.00000 0.00002 REMARK 300 0.00000 0.00002 1.00000 -0.00004 0.00000 -0.00004 -1.00000 REMARK 300 TRANSLATION 69.89 0.0094 78.9707 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 69.89000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 78.97000 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 LYS A 42 REMARK 465 GLU A 43 REMARK 465 SER A 44 REMARK 465 LYS A 45 REMARK 465 GLU A 46 REMARK 465 LYS A 47 REMARK 465 THR A 48 REMARK 465 LYS A 49 REMARK 465 GLN A 50 REMARK 465 GLY A 51 REMARK 465 GLN A 52 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 40 49.46 -79.64 REMARK 500 REMARK 500 REMARK: NULL DBREF 1SDO A 1 203 UNP Q84AF2 Q84AF2_BACST 1 203 SEQRES 1 A 203 MET ARG ILE VAL GLU VAL TYR SER HIS LEU ASN GLY LEU SEQRES 2 A 203 GLU TYR ILE GLN VAL HIS LEU PRO HIS ILE TRP GLU GLU SEQRES 3 A 203 ILE GLN GLU ILE ILE VAL SER ILE ASP ALA GLU ALA CYS SEQRES 4 A 203 ARG THR LYS GLU SER LYS GLU LYS THR LYS GLN GLY GLN SEQRES 5 A 203 ILE LEU TYR SER PRO VAL ALA LEU ASN GLU ALA PHE LYS SEQRES 6 A 203 GLU LYS LEU GLU ALA LYS GLY TRP LYS GLU SER ARG THR SEQRES 7 A 203 ASN TYR TYR VAL THR ALA ASP PRO LYS LEU ILE ARG GLU SEQRES 8 A 203 THR LEU SER LEU GLU PRO GLU GLU GLN LYS LYS VAL ILE SEQRES 9 A 203 GLU ALA ALA GLY LYS GLU ALA LEU LYS SER TYR ASN GLN SEQRES 10 A 203 THR ASP PHE VAL LYS ASP ARG VAL ALA ILE GLU VAL GLN SEQRES 11 A 203 PHE GLY LYS TYR SER PHE VAL ALA TYR ASP LEU PHE VAL SEQRES 12 A 203 LYS HIS MET ALA PHE TYR VAL SER ASP LYS ILE ASP VAL SEQRES 13 A 203 GLY VAL GLU ILE LEU PRO MET LYS GLU LEU SER LYS GLU SEQRES 14 A 203 MET SER SER GLY ILE SER TYR TYR GLU GLY GLU LEU TYR SEQRES 15 A 203 ASN VAL ILE ARG GLN GLY ARG GLY VAL PRO ALA VAL PRO SEQRES 16 A 203 LEU VAL LEU ILE GLY ILE ALA PRO FORMUL 2 HOH *90(H2 O) HELIX 1 1 ASN A 11 LEU A 20 1 10 HELIX 2 2 LEU A 20 ILE A 34 1 15 HELIX 3 3 ASP A 35 ARG A 40 5 6 HELIX 4 4 SER A 56 LYS A 71 1 16 HELIX 5 5 ASP A 85 LEU A 93 1 9 HELIX 6 6 GLU A 96 ALA A 107 1 12 HELIX 7 7 LYS A 133 VAL A 143 1 11 HELIX 8 8 VAL A 143 SER A 151 1 9 HELIX 9 9 MET A 163 LYS A 168 1 6 HELIX 10 10 TYR A 176 ARG A 186 1 11 SHEET 1 A 6 ARG A 2 HIS A 9 0 SHEET 2 A 6 LEU A 196 ALA A 202 -1 O LEU A 196 N HIS A 9 SHEET 3 A 6 VAL A 156 PRO A 162 1 N LEU A 161 O ILE A 199 SHEET 4 A 6 VAL A 125 VAL A 129 1 N GLU A 128 O ILE A 160 SHEET 5 A 6 LEU A 112 LYS A 122 -1 N PHE A 120 O ILE A 127 SHEET 6 A 6 LYS A 74 VAL A 82 -1 N VAL A 82 O LEU A 112 CISPEP 1 VAL A 191 PRO A 192 0 0.08 CRYST1 69.890 76.610 78.970 90.00 90.00 90.00 I 2 2 2 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 0.014308 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013053 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012663 0.00000