HEADER HYDROLASE 09-AUG-23 8Q5O TITLE N-TERMINAL DOMAIN OF RESTRICTION ENDONUCLEASE ECO15I WITH TETRA- TITLE 2 METHYLATED TARGET DNA. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RESTRICTION ENDONUCLEASE (ECO15I); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*TP*GP*(5CM)P*TP*GP*(5CM)P*TP*C)-3'); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(*GP*AP*GP*(5CM)P*AP*GP*(5CM)P*AP*G)-3'); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: EIL45146; SOURCE 5 GENE: GIB53_21535, IT029_004930, J5U05_004825; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS METHYLATION-DEPENDENT RESTRICTION ENZYME, DNA METHYLATION, KEYWDS 2 RESTRICTION OF MODIFIED PHAGE DNA, BISI FAMILY ENDONUCLEASES, 5- KEYWDS 3 METHYLCYTOSINE RECOGNITION, TYPE II RESTRICTION ENDONUCLEASES, KEYWDS 4 MODIFICATION-SPECIFIC RESTRICTION ENZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.RAFALSKI,K.KRAKOWSKA,M.BOCHTLER REVDAT 3 04-SEP-24 8Q5O 1 JRNL REVDAT 2 07-AUG-24 8Q5O 1 JRNL REVDAT 1 17-JUL-24 8Q5O 0 JRNL AUTH K.SZAFRAN,D.RAFALSKI,K.SKOWRONEK,M.WOJCIECHOWSKI, JRNL AUTH 2 A.A.KAZRANI,M.GILSKI,S.Y.XU,M.BOCHTLER JRNL TITL STRUCTURAL ANALYSIS OF THE BISI FAMILY OF MODIFICATION JRNL TITL 2 DEPENDENT RESTRICTION ENDONUCLEASES. JRNL REF NUCLEIC ACIDS RES. V. 52 9103 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 39041409 JRNL DOI 10.1093/NAR/GKAE634 REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0403 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22347 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.264 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.589 REMARK 3 FREE R VALUE TEST SET COUNT : 1249 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) : 2.33 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1467 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 158 REMARK 3 BIN FREE R VALUE : 0.3500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2293 REMARK 3 NUCLEIC ACID ATOMS : 367 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 127.6 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 17.78300 REMARK 3 B22 (A**2) : 17.78300 REMARK 3 B33 (A**2) : -35.56500 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): 0.067 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.049 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.246 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.928 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2734 ; 0.019 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2380 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3781 ; 1.300 ; 1.660 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5444 ; 0.672 ; 1.574 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 289 ; 4.998 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 17 ;12.881 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 359 ;20.878 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 442 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2969 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 592 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 699 ; 0.224 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 52 ; 0.385 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1287 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 99 ; 0.191 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.143 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.252 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1190 ; 6.397 ;12.938 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1186 ; 6.232 ;12.932 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1465 ; 9.179 ;23.199 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1466 ; 9.176 ;23.196 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1544 ; 5.546 ;12.670 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1544 ; 5.545 ;12.671 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2316 ; 8.186 ;23.109 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2317 ; 8.184 ;23.107 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 8 A 159 NULL REMARK 3 1 A 8 A 159 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.5235 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -K, -H, -L REMARK 3 TWIN FRACTION : 0.4765 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 8 A 160 REMARK 3 ORIGIN FOR THE GROUP (A): -39.8725 16.8879 3.3408 REMARK 3 T TENSOR REMARK 3 T11: 0.1004 T22: 0.1102 REMARK 3 T33: 0.0730 T12: 0.0156 REMARK 3 T13: 0.0061 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.0186 L22: 0.0256 REMARK 3 L33: 0.1149 L12: -0.0016 REMARK 3 L13: -0.0443 L23: 0.0180 REMARK 3 S TENSOR REMARK 3 S11: -0.0080 S12: -0.0241 S13: 0.0189 REMARK 3 S21: 0.0002 S22: 0.0273 S23: 0.0336 REMARK 3 S31: 0.0388 S32: 0.0692 S33: -0.0192 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): -59.4742 28.9988 2.8345 REMARK 3 T TENSOR REMARK 3 T11: 0.1027 T22: 0.0922 REMARK 3 T33: 0.0736 T12: -0.0101 REMARK 3 T13: -0.0019 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 0.0781 L22: 0.0297 REMARK 3 L33: 0.1184 L12: -0.0265 REMARK 3 L13: -0.0108 L23: 0.0507 REMARK 3 S TENSOR REMARK 3 S11: -0.0034 S12: -0.0015 S13: 0.0023 REMARK 3 S21: 0.0021 S22: 0.0040 S23: 0.0119 REMARK 3 S31: 0.0002 S32: 0.0146 S33: -0.0006 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): -54.3573 18.3885 3.9228 REMARK 3 T TENSOR REMARK 3 T11: 0.1043 T22: 0.0814 REMARK 3 T33: 0.0919 T12: -0.0076 REMARK 3 T13: 0.0121 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.0180 L22: 0.0079 REMARK 3 L33: 0.3539 L12: -0.0039 REMARK 3 L13: 0.0241 L23: 0.0406 REMARK 3 S TENSOR REMARK 3 S11: 0.0195 S12: 0.0066 S13: 0.0289 REMARK 3 S21: 0.0029 S22: 0.0096 S23: -0.0177 REMARK 3 S31: 0.0726 S32: -0.0156 S33: -0.0290 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): -51.7328 16.9174 2.0996 REMARK 3 T TENSOR REMARK 3 T11: 0.0934 T22: 0.0823 REMARK 3 T33: 0.1050 T12: -0.0024 REMARK 3 T13: 0.0201 T23: -0.0231 REMARK 3 L TENSOR REMARK 3 L11: 0.0266 L22: 0.1594 REMARK 3 L33: 0.2917 L12: -0.0012 REMARK 3 L13: -0.0765 L23: 0.0652 REMARK 3 S TENSOR REMARK 3 S11: -0.0396 S12: -0.0011 S13: -0.0290 REMARK 3 S21: 0.0327 S22: -0.0059 S23: 0.0329 REMARK 3 S31: 0.0321 S32: 0.0346 S33: 0.0456 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8Q5O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292131559. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22349 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 47.998 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 19.60 REMARK 200 R MERGE (I) : 0.10960 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 20.60 REMARK 200 R MERGE FOR SHELL (I) : 1.29400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.330 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: P 32 2 1 REMARK 200 96 96 96.3 REMARK 200 90 90 120 REMARK 200 CRYSTAL WAS A MEROHYDRAL TWIN REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 6.5, 0.02 M CACL2, 35 REMARK 280 % PENTAERYTHRITOL ETHOXYLATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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 64.20467 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 32.10233 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 32.10233 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 64.20467 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A 6 REMARK 465 SER A 7 REMARK 465 LEU A 21 REMARK 465 LYS A 81 REMARK 465 PRO A 87 REMARK 465 THR A 116 REMARK 465 LYS A 161 REMARK 465 GLU A 162 REMARK 465 ASP A 163 REMARK 465 LEU A 164 REMARK 465 ILE A 165 REMARK 465 VAL A 166 REMARK 465 ARG A 167 REMARK 465 SER A 168 REMARK 465 SER A 169 REMARK 465 ALA A 170 REMARK 465 SER A 171 REMARK 465 VAL A 172 REMARK 465 ASN A 173 REMARK 465 GLU A 174 REMARK 465 ALA A 175 REMARK 465 ALA A 176 REMARK 465 MET A 177 REMARK 465 GLN A 178 REMARK 465 THR A 179 REMARK 465 GLY B 6 REMARK 465 SER B 7 REMARK 465 ASP B 88 REMARK 465 ILE B 160 REMARK 465 LYS B 161 REMARK 465 GLU B 162 REMARK 465 ASP B 163 REMARK 465 LEU B 164 REMARK 465 ILE B 165 REMARK 465 VAL B 166 REMARK 465 ARG B 167 REMARK 465 SER B 168 REMARK 465 SER B 169 REMARK 465 ALA B 170 REMARK 465 SER B 171 REMARK 465 VAL B 172 REMARK 465 ASN B 173 REMARK 465 GLU B 174 REMARK 465 ALA B 175 REMARK 465 ALA B 176 REMARK 465 MET B 177 REMARK 465 GLN B 178 REMARK 465 THR B 179 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR A 9 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE A 27 CG1 CG2 CD1 REMARK 470 ARG A 32 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 40 CG CD CE NZ REMARK 470 ASN A 42 CG OD1 ND2 REMARK 470 LEU A 51 CG CD1 CD2 REMARK 470 THR A 59 OG1 CG2 REMARK 470 ASN A 63 CG OD1 ND2 REMARK 470 ASP A 106 CG OD1 OD2 REMARK 470 ARG A 131 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 17 CG OD1 ND2 REMARK 470 ARG B 32 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 40 CG CD CE NZ REMARK 470 ASN B 41 CG OD1 ND2 REMARK 470 SER B 65 OG REMARK 470 THR B 86 OG1 CG2 REMARK 470 TYR B 100 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 148 CG CD CE NZ REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ALA B 82 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 TYR A 9 N CA CB REMARK 480 LEU A 60 CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASP A 88 O PRO B 87 3455 1.29 REMARK 500 OD1 ASP A 88 C PRO B 87 3455 1.47 REMARK 500 CG ASP A 88 O PRO B 87 3455 1.93 REMARK 500 REMARK 500 REMARK: NULL 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 DT C 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT C 2 C3' - O3' - P ANGL. DEV. = -8.8 DEGREES REMARK 500 DG C 3 C3' - O3' - P ANGL. DEV. = -10.3 DEGREES REMARK 500 5CM C 4 C3' - O3' - P ANGL. DEV. = -12.5 DEGREES REMARK 500 DT C 5 C3' - O3' - P ANGL. DEV. = -7.4 DEGREES REMARK 500 DA D 2 C3' - O3' - P ANGL. DEV. = -11.1 DEGREES REMARK 500 DG D 3 C3' - O3' - P ANGL. DEV. = -10.0 DEGREES REMARK 500 5CM D 4 C3' - O3' - P ANGL. DEV. = -10.5 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 LYS A 40 40.14 -89.33 REMARK 500 SER A 64 2.42 -66.67 REMARK 500 ALA A 66 55.93 26.39 REMARK 500 ALA A 68 -167.34 -71.12 REMARK 500 LEU A 120 -58.16 -121.74 REMARK 500 TYR A 133 32.70 -141.95 REMARK 500 TYR B 9 48.31 -97.94 REMARK 500 ASN B 41 -153.37 -86.75 REMARK 500 ALA B 103 67.22 63.85 REMARK 500 LEU B 147 77.24 -110.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 83 0.12 SIDE CHAIN REMARK 500 ARG A 84 0.14 SIDE CHAIN REMARK 500 ARG B 38 0.10 SIDE CHAIN REMARK 500 ARG B 84 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 69 OD2 REMARK 620 2 GLN A 79 OE1 57.7 REMARK 620 3 HOH A 303 O 121.2 168.7 REMARK 620 4 DA D 5 OP1 95.9 73.5 117.3 REMARK 620 5 HOH D 101 O 148.8 91.0 89.1 74.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 69 OD2 REMARK 620 2 GLN B 79 OE1 67.6 REMARK 620 3 ILE B 80 O 80.3 69.8 REMARK 620 4 DT C 5 OP1 76.4 87.6 152.4 REMARK 620 5 HOH C 101 O 144.5 87.5 115.5 77.8 REMARK 620 6 HOH C 102 O 111.3 144.7 75.2 127.3 103.6 REMARK 620 N 1 2 3 4 5 DBREF1 8Q5O A 8 179 UNP A0A0L6ZWS4_ECOLX DBREF2 8Q5O A A0A0L6ZWS4 8 179 DBREF1 8Q5O B 8 179 UNP A0A0L6ZWS4_ECOLX DBREF2 8Q5O B A0A0L6ZWS4 8 179 DBREF 8Q5O C 1 9 PDB 8Q5O 8Q5O 1 9 DBREF 8Q5O D 1 9 PDB 8Q5O 8Q5O 1 9 SEQADV 8Q5O GLY A 6 UNP A0A0L6ZWS EXPRESSION TAG SEQADV 8Q5O SER A 7 UNP A0A0L6ZWS EXPRESSION TAG SEQADV 8Q5O GLY B 6 UNP A0A0L6ZWS EXPRESSION TAG SEQADV 8Q5O SER B 7 UNP A0A0L6ZWS EXPRESSION TAG SEQRES 1 A 174 GLY SER SER TYR ASP TRP LEU ASN ALA LEU ASN ASN LEU SEQRES 2 A 174 GLU LEU LEU SER LEU HIS SER GLU ILE LEU THR GLN LEU SEQRES 3 A 174 ARG SER ARG GLY VAL ILE ARG THR LYS ASN ASN PRO VAL SEQRES 4 A 174 GLY ASP TYR ALA GLU TRP LEU VAL SER ASN ALA LEU GLY SEQRES 5 A 174 MET THR LEU LEU SER ASN SER SER ALA GLY ALA ASP ALA SEQRES 6 A 174 ILE ASP ALA ASP GLY LEU LYS VAL GLN ILE LYS ALA ARG SEQRES 7 A 174 ARG VAL THR PRO ASP ASN PRO SER ARG GLN LEU SER ALA SEQRES 8 A 174 LEU ARG ASN TYR GLU ALA ALA ASP PHE ASP TYR LEU ILE SEQRES 9 A 174 ALA VAL ILE PHE ASP GLU THR TYR ASN ILE LEU ASP ALA SEQRES 10 A 174 TYR LYS ILE PRO HIS GLU VAL ILE ARG ASP TYR ALA ARG SEQRES 11 A 174 HIS SER ASP HIS VAL ASN ALA HIS ILE VAL ASN LEU LYS SEQRES 12 A 174 GLY ALA ILE LEU THR ASP PRO ARG VAL SER SER ILE LYS SEQRES 13 A 174 GLU ASP LEU ILE VAL ARG SER SER ALA SER VAL ASN GLU SEQRES 14 A 174 ALA ALA MET GLN THR SEQRES 1 B 174 GLY SER SER TYR ASP TRP LEU ASN ALA LEU ASN ASN LEU SEQRES 2 B 174 GLU LEU LEU SER LEU HIS SER GLU ILE LEU THR GLN LEU SEQRES 3 B 174 ARG SER ARG GLY VAL ILE ARG THR LYS ASN ASN PRO VAL SEQRES 4 B 174 GLY ASP TYR ALA GLU TRP LEU VAL SER ASN ALA LEU GLY SEQRES 5 B 174 MET THR LEU LEU SER ASN SER SER ALA GLY ALA ASP ALA SEQRES 6 B 174 ILE ASP ALA ASP GLY LEU LYS VAL GLN ILE LYS ALA ARG SEQRES 7 B 174 ARG VAL THR PRO ASP ASN PRO SER ARG GLN LEU SER ALA SEQRES 8 B 174 LEU ARG ASN TYR GLU ALA ALA ASP PHE ASP TYR LEU ILE SEQRES 9 B 174 ALA VAL ILE PHE ASP GLU THR TYR ASN ILE LEU ASP ALA SEQRES 10 B 174 TYR LYS ILE PRO HIS GLU VAL ILE ARG ASP TYR ALA ARG SEQRES 11 B 174 HIS SER ASP HIS VAL ASN ALA HIS ILE VAL ASN LEU LYS SEQRES 12 B 174 GLY ALA ILE LEU THR ASP PRO ARG VAL SER SER ILE LYS SEQRES 13 B 174 GLU ASP LEU ILE VAL ARG SER SER ALA SER VAL ASN GLU SEQRES 14 B 174 ALA ALA MET GLN THR SEQRES 1 C 9 DC DT DG 5CM DT DG 5CM DT DC SEQRES 1 D 9 DG DA DG 5CM DA DG 5CM DA DG HET 5CM C 4 20 HET 5CM C 7 20 HET 5CM D 4 20 HET 5CM D 7 20 HET CA A 201 1 HET CA B 201 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM CA CALCIUM ION FORMUL 3 5CM 4(C10 H16 N3 O7 P) FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *24(H2 O) HELIX 1 AA1 TYR A 9 ALA A 14 5 6 HELIX 2 AA2 GLU A 19 LEU A 20 5 2 HELIX 3 AA3 SER A 22 SER A 22 5 1 HELIX 4 AA4 LEU A 23 ARG A 34 1 12 HELIX 5 AA5 ASN A 42 GLY A 57 1 16 HELIX 6 AA6 ASN A 99 ALA A 103 5 5 HELIX 7 AA7 HIS A 127 ASP A 132 1 6 HELIX 8 AA8 GLY A 149 ASP A 154 5 6 HELIX 9 AA9 ASP B 10 LEU B 15 5 6 HELIX 10 AB1 ASN B 16 ARG B 34 1 19 HELIX 11 AB2 ASN B 42 GLY B 57 1 16 HELIX 12 AB3 HIS B 127 ASP B 132 1 6 HELIX 13 AB4 GLY B 149 ASP B 154 1 6 SHEET 1 AA1 5 THR A 59 LEU A 60 0 SHEET 2 AA1 5 ALA A 70 ILE A 71 -1 O ILE A 71 N THR A 59 SHEET 3 AA1 5 LYS A 77 GLN A 79 -1 O VAL A 78 N ALA A 70 SHEET 4 AA1 5 TYR A 107 PHE A 113 1 O ILE A 109 N GLN A 79 SHEET 5 AA1 5 ARG A 83 ARG A 84 1 N ARG A 83 O PHE A 113 SHEET 1 AA2 6 THR A 59 LEU A 60 0 SHEET 2 AA2 6 ALA A 70 ILE A 71 -1 O ILE A 71 N THR A 59 SHEET 3 AA2 6 LYS A 77 GLN A 79 -1 O VAL A 78 N ALA A 70 SHEET 4 AA2 6 TYR A 107 PHE A 113 1 O ILE A 109 N GLN A 79 SHEET 5 AA2 6 ILE A 119 PRO A 126 -1 O TYR A 123 N ALA A 110 SHEET 6 AA2 6 SER A 158 SER A 159 -1 O SER A 158 N LYS A 124 SHEET 1 AA3 2 ARG A 135 SER A 137 0 SHEET 2 AA3 2 ALA A 142 ILE A 144 -1 O ILE A 144 N ARG A 135 SHEET 1 AA4 5 MET B 58 LEU B 60 0 SHEET 2 AA4 5 ALA B 70 ASP B 72 -1 O ILE B 71 N THR B 59 SHEET 3 AA4 5 LYS B 77 ARG B 84 -1 O VAL B 78 N ALA B 70 SHEET 4 AA4 5 TYR B 107 PHE B 113 1 O PHE B 113 N ARG B 83 SHEET 5 AA4 5 ILE B 119 PRO B 126 -1 O ASP B 121 N ILE B 112 SHEET 1 AA5 2 ARG B 135 SER B 137 0 SHEET 2 AA5 2 ALA B 142 ILE B 144 -1 O ILE B 144 N ARG B 135 LINK O3' DG C 3 P 5CM C 4 1555 1555 1.60 LINK O3' 5CM C 4 P DT C 5 1555 1555 1.60 LINK O3' DG C 6 P 5CM C 7 1555 1555 1.61 LINK O3' 5CM C 7 P DT C 8 1555 1555 1.60 LINK O3' DG D 3 P 5CM D 4 1555 1555 1.60 LINK O3' 5CM D 4 P DA D 5 1555 1555 1.60 LINK O3' DG D 6 P 5CM D 7 1555 1555 1.61 LINK O3' 5CM D 7 P DA D 8 1555 1555 1.61 LINK OD2 ASP A 69 CA CA A 201 1555 1555 2.59 LINK OE1 GLN A 79 CA CA A 201 1555 1555 2.72 LINK CA CA A 201 O HOH A 303 1555 1555 2.54 LINK CA CA A 201 OP1 DA D 5 1555 1555 2.35 LINK CA CA A 201 O HOH D 101 1555 1555 2.86 LINK OD2 ASP B 69 CA CA B 201 1555 1555 2.25 LINK OE1 GLN B 79 CA CA B 201 1555 1555 2.57 LINK O ILE B 80 CA CA B 201 1555 1555 2.11 LINK CA CA B 201 OP1 DT C 5 1555 1555 2.18 LINK CA CA B 201 O HOH C 101 1555 1555 2.51 LINK CA CA B 201 O HOH C 102 1555 1555 2.77 CRYST1 95.995 95.995 96.307 90.00 90.00 120.00 P 32 2 1 12 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 0.010417 0.006014 0.000000 0.00000 SCALE2 0.000000 0.012029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010383 0.00000