HEADER DNA BINDING PROTEIN 02-MAR-21 7E8R TITLE ECOT38I RESTRICTION ENDONUCLEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ECOT38I RESTRICTION ENDONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE P2; SOURCE 3 ORGANISM_COMMON: BACTERIOPHAGE P2; SOURCE 4 ORGANISM_TAXID: 10679; SOURCE 5 GENE: ECOT38IR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET3A KEYWDS ENDONUCLEASE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.KITA,B.MIKAMI REVDAT 2 16-OCT-24 7E8R 1 REMARK REVDAT 1 02-MAR-22 7E8R 0 JRNL AUTH K.KITA,B.MIKAMI JRNL TITL STRUCTURAL ANALYSIS OF ECOT38I RESTRICTION ENDONUCLEASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 33626 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1680 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.2000 - 4.3400 1.00 2915 153 0.1811 0.2212 REMARK 3 2 4.3400 - 3.4500 1.00 2744 145 0.1702 0.1972 REMARK 3 3 3.4500 - 3.0100 1.00 2688 141 0.1930 0.2361 REMARK 3 4 3.0100 - 2.7400 1.00 2675 141 0.2123 0.2516 REMARK 3 5 2.7400 - 2.5400 1.00 2638 139 0.2188 0.2928 REMARK 3 6 2.5400 - 2.3900 1.00 2654 139 0.2132 0.2872 REMARK 3 7 2.3900 - 2.2700 1.00 2639 139 0.2207 0.2559 REMARK 3 8 2.2700 - 2.1700 1.00 2630 139 0.2180 0.2552 REMARK 3 9 2.1700 - 2.0900 1.00 2616 137 0.2220 0.2533 REMARK 3 10 2.0900 - 2.0200 1.00 2606 138 0.2277 0.2872 REMARK 3 11 2.0200 - 1.9500 1.00 2607 137 0.2489 0.2948 REMARK 3 12 1.9500 - 1.9000 0.98 2534 132 0.2839 0.2997 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.226 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.829 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2845 REMARK 3 ANGLE : 0.735 3857 REMARK 3 CHIRALITY : 0.054 452 REMARK 3 PLANARITY : 0.004 488 REMARK 3 DIHEDRAL : 18.952 1048 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7E8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300020985. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33635 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THIN PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG6000, 5% MPD, 0.1M HEPES, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 166.66667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 83.33333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 83.33333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 166.66667 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 166.66667 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 PRO A 171 REMARK 465 ASN A 172 REMARK 465 SER A 173 REMARK 465 LEU A 318 REMARK 465 LEU A 319 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 LYS A 28 38.15 -95.77 REMARK 500 ARG A 115 54.07 -91.58 REMARK 500 ASN A 166 53.67 -113.30 REMARK 500 PRO A 189 99.77 -67.96 REMARK 500 REMARK 500 REMARK: NULL DBREF 7E8R A 1 351 UNP Q83VS8 Q83VS8_BPP2 1 351 SEQRES 1 A 351 MET LYS VAL LEU VAL ASN HIS GLU GLN ALA TYR ASN VAL SEQRES 2 A 351 ILE ILE ASN ALA ILE ASN ASP ALA LYS LYS LEU THR ASP SEQRES 3 A 351 TYR LYS THR ASN ASN GLN TRP VAL SER ILE GLN ASN VAL SEQRES 4 A 351 ILE LEU GLY THR HIS LEU THR TYR ARG TYR ILE LEU ILE SEQRES 5 A 351 THR GLY LEU LEU ALA LYS ALA THR ASP PRO ARG VAL ASN SEQRES 6 A 351 PRO LEU ALA LEU GLN ALA ASN ALA PRO VAL ASP GLY ALA SEQRES 7 A 351 TYR ASP ALA ARG SER LEU CYS HIS SER VAL ILE VAL GLY SEQRES 8 A 351 LYS VAL GLU GLY PRO PHE LEU GLU GLY LYS LEU GLY ALA SEQRES 9 A 351 SER ASN GLU PRO PHE LEU ASN LYS PRO ALA ARG TYR MET SEQRES 10 A 351 LEU HIS SER SER ASP ASN PRO VAL ARG ARG GLY ASN ASP SEQRES 11 A 351 LYS VAL LEU GLN GLN LEU SER ILE ASP ILE LEU HIS ALA SEQRES 12 A 351 ALA THR THR GLN THR LEU ALA TYR GLU MET LEU VAL ILE SEQRES 13 A 351 ALA LEU TYR PHE THR LEU GLN ARG THR ASN ARG VAL ILE SEQRES 14 A 351 THR PRO ASN SER ILE ASN PHE ASP PHE HIS LYS ILE ILE SEQRES 15 A 351 TYR ASN ILE ILE SER HIS PRO CYS ASP GLY GLU THR CYS SEQRES 16 A 351 ALA ILE ALA ALA ALA ILE SER LEU HIS LEU LEU GLY GLU SEQRES 17 A 351 GLN ARG GLY TRP ILE ILE LYS ALA HIS PRO VAL ASN GLN SEQRES 18 A 351 ALA GLY SER SER SER LYS GLU ILE LEU ASP ILE ASP VAL SEQRES 19 A 351 TYR HIS ASP ASP ILE VAL PHE LEU SER ILE GLU VAL LYS SEQRES 20 A 351 ASP LYS PRO PHE ASN TYR GLN ASP VAL ASN HIS ALA VAL SEQRES 21 A 351 SER LYS ALA SER ALA SER GLY ILE SER LYS VAL ILE PHE SEQRES 22 A 351 LEU LYS GLY PRO ARG ALA THR ASN LEU ASP ILE ASP GLU SEQRES 23 A 351 SER LEU ALA ILE GLU ASN ALA ALA THR LYS GLY VAL SER SEQRES 24 A 351 LEU SER PHE SER ASP VAL MET THR PHE THR THR THR CYS SEQRES 25 A 351 TYR ALA LEU SER PRO LEU LEU SER ASN ASP ARG ILE ILE SEQRES 26 A 351 ASP PHE ILE ASN ASN THR LEU LYS ASP ILE ARG ALA LYS SEQRES 27 A 351 ASP SER THR ILE GLU TYR ILE GLN SER ILE PHE LYS ASN HET GOL A 401 6 HET GOL A 402 6 HET GOL A 403 6 HET GOL A 404 6 HET GOL A 405 6 HET GOL A 406 6 HET GOL A 407 6 HET GOL A 408 6 HET GOL A 409 6 HET GOL A 410 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 10(C3 H8 O3) FORMUL 12 HOH *274(H2 O) HELIX 1 AA1 ASN A 6 LYS A 23 1 18 HELIX 2 AA2 GLN A 32 GLY A 42 1 11 HELIX 3 AA3 HIS A 44 ASP A 61 1 18 HELIX 4 AA4 ASP A 80 VAL A 88 1 9 HELIX 5 AA5 VAL A 88 VAL A 93 1 6 HELIX 6 AA6 VAL A 93 GLU A 99 1 7 HELIX 7 AA7 GLU A 107 ARG A 115 5 9 HELIX 8 AA8 GLY A 128 ALA A 144 1 17 HELIX 9 AA9 THR A 146 LEU A 162 1 17 HELIX 10 AB1 ASP A 177 HIS A 188 1 12 HELIX 11 AB2 GLY A 192 GLU A 208 1 17 HELIX 12 AB3 GLN A 209 GLY A 211 5 3 HELIX 13 AB4 ASN A 252 GLY A 267 1 16 HELIX 14 AB5 PRO A 277 THR A 280 5 4 HELIX 15 AB6 ASP A 285 LYS A 296 1 12 HELIX 16 AB7 VAL A 305 LEU A 315 1 11 HELIX 17 AB8 ARG A 323 ILE A 335 1 13 HELIX 18 AB9 LYS A 338 ASN A 351 1 14 SHEET 1 AA1 5 ILE A 213 ALA A 216 0 SHEET 2 AA1 5 LEU A 230 HIS A 236 -1 O TYR A 235 N ILE A 213 SHEET 3 AA1 5 ILE A 239 LYS A 247 -1 O ILE A 244 N ILE A 232 SHEET 4 AA1 5 LYS A 270 LYS A 275 1 O LEU A 274 N GLU A 245 SHEET 5 AA1 5 SER A 299 ASP A 304 1 O SER A 301 N PHE A 273 SSBOND 1 CYS A 190 CYS A 195 1555 1555 2.05 CRYST1 53.159 53.159 250.000 90.00 90.00 120.00 P 32 2 1 6 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 0.018811 0.010861 0.000000 0.00000 SCALE2 0.000000 0.021722 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004000 0.00000