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, AUTHOR 2 C.R.ESCALANTE,S.Y.XU,A.K.AGGARWAL 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 JRNL TITL 3 OVERLAPPING 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 1 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) : 1.29 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.93 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.83 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. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-04. REMARK 100 THE RCSB ID CODE IS RCSB021620. 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 : 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 REMARK 280 CALCIUM CHLORIDE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 MASTER 270 0 0 10 6 0 0 6 0 0 0 16 END