PDB Short entry for 1CL8 HEADER PROTEIN/DNA 06-MAY-99 1CL8 TITLE A PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAPTTCGCG) TITLE 2 COMPLEX WITH DNA BASE ANALOG PURINE (P) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*CP*GP*CP*GP*AP*(PRN)P*TP*TP*CP*GP*CP*G)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROTEIN (ENDONUCLEASE); COMPND 7 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 5 ORGANISM_TAXID: 562 KEYWDS ENDONUCLEASE/DNA, DNA BASE ANALOG, PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.HORVATH,J.M.ROSENBERG REVDAT 3 09-AUG-23 1CL8 1 LINK REVDAT 2 24-FEB-09 1CL8 1 VERSN REVDAT 1 19-MAY-99 1CL8 0 JRNL AUTH M.HORVATH,J.M.ROSENBERG JRNL TITL IAP (INNER-ADENINE TO PURINE): A COGNATE ECORI-DNA BASE JRNL TITL 2 ANALOG COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 35192 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : RFREE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3528 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2898 REMARK 3 BIN R VALUE (WORKING SET) : 0.3568 REMARK 3 BIN FREE R VALUE : 0.3576 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 326 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 : 2051 REMARK 3 NUCLEIC ACID ATOMS : 262 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 155 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.10 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM SIGMAA (A) : 0.28 REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.067 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 0.805 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM11.WAT REMARK 3 PARAMETER FILE 3 : MODIFIED DNA-RNA.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.PEP REMARK 3 TOPOLOGY FILE 3 : TOPH11.WAT REMARK 3 TOPOLOGY FILE 4 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DNA-RNA.PARAM WAS MODIFIED TO CONTAIN A REMARK 3 MODIFIED RESIDUE PRN REMARK 4 REMARK 4 1CL8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000001015. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-98 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 : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35192 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.43200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1CKQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -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 0.00000 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 0.00000 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 0.00000 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 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 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 APPLY THE FOLLOWING TO CHAINS: B, 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 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 SER A 2 REMARK 465 ASN A 3 REMARK 465 LYS A 4 REMARK 465 LYS A 5 REMARK 465 GLN A 6 REMARK 465 SER A 7 REMARK 465 ASN A 8 REMARK 465 ARG A 9 REMARK 465 LEU A 10 REMARK 465 THR A 11 REMARK 465 GLU A 12 REMARK 465 GLN A 13 REMARK 465 HIS A 14 REMARK 465 LYS A 15 REMARK 465 LEU A 16 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 LEU A 81 98.06 -169.11 REMARK 500 GLN A 115 132.93 -170.88 REMARK 500 ASP A 133 -11.43 -144.20 REMARK 500 PRO A 164 48.50 -79.07 REMARK 500 ASN A 224 143.23 176.81 REMARK 500 ASP A 227 86.31 -69.19 REMARK 500 LYS A 228 -58.89 -134.77 REMARK 500 SER A 229 118.09 77.61 REMARK 500 THR A 275 -68.49 -99.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 PRN IS ADENINE WITH THE N6 AMINO GROUP REMOVED REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: PER REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: PROTEIN RECOGNTION RESIDUES INVOLVED IN HYDROGEN REMARK 800 BONDING CONTACTS AT THE SITE OF PERTURBATION REMARK 800 REMARK 800 SITE_IDENTIFIER: DNA REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: DNA RECOGNITION SEQUENCE DBREF 1CL8 A 2 277 UNP P00642 T2E1_ECOLI 1 276 DBREF 1CL8 B 1 13 PDB 1CL8 1CL8 1 13 SEQRES 1 B 13 DT DC DG DC DG DA PRN DT DT DC DG DC DG SEQRES 1 A 276 SER ASN LYS LYS GLN SER ASN ARG LEU THR GLU GLN HIS SEQRES 2 A 276 LYS LEU SER GLN GLY VAL ILE GLY ILE PHE GLY ASP TYR SEQRES 3 A 276 ALA LYS ALA HIS ASP LEU ALA VAL GLY GLU VAL SER LYS SEQRES 4 A 276 LEU VAL LYS LYS ALA LEU SER ASN GLU TYR PRO GLN LEU SEQRES 5 A 276 SER PHE ARG TYR ARG ASP SER ILE LYS LYS THR GLU ILE SEQRES 6 A 276 ASN GLU ALA LEU LYS LYS ILE ASP PRO ASP LEU GLY GLY SEQRES 7 A 276 THR LEU PHE VAL SER ASN SER SER ILE LYS PRO ASP GLY SEQRES 8 A 276 GLY ILE VAL GLU VAL LYS ASP ASP TYR GLY GLU TRP ARG SEQRES 9 A 276 VAL VAL LEU VAL ALA GLU ALA LYS HIS GLN GLY LYS ASP SEQRES 10 A 276 ILE ILE ASN ILE ARG ASN GLY LEU LEU VAL GLY LYS ARG SEQRES 11 A 276 GLY ASP GLN ASP LEU MET ALA ALA GLY ASN ALA ILE GLU SEQRES 12 A 276 ARG SER HIS LYS ASN ILE SER GLU ILE ALA ASN PHE MET SEQRES 13 A 276 LEU SER GLU SER HIS PHE PRO TYR VAL LEU PHE LEU GLU SEQRES 14 A 276 GLY SER ASN PHE LEU THR GLU ASN ILE SER ILE THR ARG SEQRES 15 A 276 PRO ASP GLY ARG VAL VAL ASN LEU GLU TYR ASN SER GLY SEQRES 16 A 276 ILE LEU ASN ARG LEU ASP ARG LEU THR ALA ALA ASN TYR SEQRES 17 A 276 GLY MET PRO ILE ASN SER ASN LEU CYS ILE ASN LYS PHE SEQRES 18 A 276 VAL ASN HIS LYS ASP LYS SER ILE MET LEU GLN ALA ALA SEQRES 19 A 276 SER ILE TYR THR GLN GLY ASP GLY ARG GLU TRP ASP SER SEQRES 20 A 276 LYS ILE MET PHE GLU ILE MET PHE ASP ILE SER THR THR SEQRES 21 A 276 SER LEU ARG VAL LEU GLY ARG ASP LEU PHE GLU GLN LEU SEQRES 22 A 276 THR SER LYS MODRES 1CL8 PRN B 7 DA PURINE 2'-DEOXYRIBO-5'-MONOPHOSPHATE HET PRN B 7 20 HETNAM PRN PURINE 2'-DEOXYRIBO-5'-MONOPHOSPHATE FORMUL 1 PRN C10 H13 N4 O6 P FORMUL 3 HOH *155(H2 O) HELIX 1 1 GLY A 19 HIS A 31 5 13 HELIX 2 2 VAL A 35 GLU A 49 1 15 HELIX 3 3 LYS A 63 ILE A 73 1 11 HELIX 4 4 ASP A 118 ARG A 123 1 6 HELIX 5 5 ALA A 142 PHE A 156 5 15 HELIX 6 6 LEU A 201 ARG A 203 5 3 HELIX 7 7 THR A 205 ASN A 208 5 4 HELIX 8 8 SER A 248 VAL A 265 1 18 HELIX 9 9 GLY A 267 ASP A 269 5 3 HELIX 10 10 PHE A 271 THR A 275 1 5 SHEET 1 A 5 PHE A 55 ARG A 58 0 SHEET 2 A 5 ILE A 94 LYS A 98 -1 N GLU A 96 O ARG A 56 SHEET 3 A 5 TRP A 104 HIS A 114 -1 N LEU A 108 O VAL A 95 SHEET 4 A 5 TYR A 165 GLU A 170 1 N VAL A 166 O VAL A 109 SHEET 5 A 5 SER A 236 GLN A 240 1 N SER A 236 O LEU A 167 SHEET 1 B 2 ILE A 179 THR A 182 0 SHEET 2 B 2 VAL A 188 LEU A 191 -1 N LEU A 191 O ILE A 179 SHEET 1 C 2 LYS A 221 VAL A 223 0 SHEET 2 C 2 ILE A 230 LEU A 232 -1 N LEU A 232 O LYS A 221 LINK O3' DA B 6 P PRN B 7 1555 1555 1.60 LINK O3' PRN B 7 P DT B 8 1555 1555 1.61 SITE 1 PER 6 ALA A 142 ASN A 141 DA B 6 PRN B 7 SITE 2 PER 6 DT B 8 DT B 9 SITE 1 DNA 6 DG B 5 DA B 6 PRN B 7 DT B 8 SITE 2 DNA 6 DT B 9 DC B 10 CRYST1 117.833 117.833 48.989 90.00 90.00 120.00 P 3 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 0.008486 0.004900 0.000000 0.00000 SCALE2 0.000000 0.009799 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020413 0.00000