HEADER DNA BINDING PROTEIN 25-FEB-25 9M1E TITLE CRYSTAL STRUCTURE OF THE CPS-6 H148A/F122A VERSUS CIS-RESVERATROL TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE G, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 63-305; COMPND 5 SYNONYM: ENDO G,CED-3 PROTEASE SUPPRESSOR 6; COMPND 6 EC: 3.1.30.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: N-TERMINAL 6XHISTIDINE TAGGED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: CPS-6, C41D11.8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI M15; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1007065; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS COMPLEX, MITOCHONDRIAL AND ENDORIBONUCLEASE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.J.LIN,H.S.YUAN REVDAT 1 04-MAR-26 9M1E 0 JRNL AUTH L.J.LIN,H.S.YUAN JRNL TITL CRYSTAL STRUCTURE OF THE CPS-6 H148A/F122A VERSUS JRNL TITL 2 CIS-RESVERATROL COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.J.LIN,C.C.WU,W.Z.YANG,H.S.YUAN REMARK 1 TITL CRYSTAL STRUCTURE OF ENDONUCLEASE G IN COMPLEX WITH DNA REMARK 1 TITL 2 REVEALS HOW IT NONSPECIFICALLY DEGRADES DNA AS A HOMODIMER REMARK 1 REF NUCLEIC ACIDS RES. V. 44 10480 2016 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 27738134 REMARK 1 DOI 10.1093/NAR/GKW931 REMARK 2 REMARK 2 RESOLUTION. 2.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12-2829 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 9976 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 9M1E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1300056972. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.62 REMARK 200 MONOCHROMATOR : LN2 COOLED SI(111) DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR (DCM) REMARK 200 OPTICS : A SI(111) DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR (DCM) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 V 706 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 V 706 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10238 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.990 REMARK 200 RESOLUTION RANGE LOW (A) : 29.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.15800 REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45600 REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.12-2829 REMARK 200 STARTING MODEL: 5GKP REMARK 200 REMARK 200 REMARK: THIN PLATE SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, 30% (W/V) PEG 1000, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 279K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 22.92800 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 54 REMARK 465 HIS A 55 REMARK 465 HIS A 56 REMARK 465 HIS A 57 REMARK 465 HIS A 58 REMARK 465 HIS A 59 REMARK 465 HIS A 60 REMARK 465 GLY A 61 REMARK 465 SER A 62 REMARK 465 LYS A 110 REMARK 465 HIS A 111 REMARK 465 ALA A 112 REMARK 465 GLU A 113 REMARK 465 GLY A 114 REMARK 465 GLY A 304 REMARK 465 GLY A 305 REMARK 465 MET B 54 REMARK 465 HIS B 55 REMARK 465 HIS B 56 REMARK 465 HIS B 57 REMARK 465 HIS B 58 REMARK 465 HIS B 59 REMARK 465 LYS B 303 REMARK 465 GLY B 304 REMARK 465 GLY B 305 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 GLU A 107 CG CD OE1 OE2 REMARK 470 ARG A 117 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 118 CG CD CE NZ REMARK 470 ARG A 156 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU B 102 HD22 ASN B 154 1.45 REMARK 500 H GLY B 178 OD2 ASP B 182 1.58 REMARK 500 OD1 ASP A 125 OG1 THR A 127 2.08 REMARK 500 REMARK 500 REMARK: NULL 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 OH TYR B 167 OD2 ASP B 228 2656 2.15 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 TYR A 209 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 TYR A 209 CB - CG - CD1 ANGL. DEV. = 4.6 DEGREES REMARK 500 PHE A 238 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 PHE A 238 CB - CG - CD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 THR A 246 C - N - CA ANGL. DEV. = 16.6 DEGREES REMARK 500 ILE A 268 CA - CB - CG1 ANGL. DEV. = -12.4 DEGREES REMARK 500 LYS A 302 CG - CD - CE ANGL. DEV. = -18.9 DEGREES REMARK 500 ARG B 108 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG B 108 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 108 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 146 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 177 CG - CD - NE ANGL. DEV. = -12.8 DEGREES REMARK 500 TYR B 202 CB - CG - CD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 TYR B 202 CD1 - CG - CD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 TYR B 202 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 GLU B 253 CG - CD - OE2 ANGL. DEV. = -12.6 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 ARG A 95 71.84 33.61 REMARK 500 THR A 96 -161.23 -167.57 REMARK 500 TRP A 99 153.82 178.60 REMARK 500 GLU A 107 -51.82 -22.80 REMARK 500 LYS A 118 36.20 -148.28 REMARK 500 LEU A 119 47.97 -109.06 REMARK 500 ALA A 122 118.96 100.76 REMARK 500 ARG A 156 2.13 -65.92 REMARK 500 PRO A 173 103.72 -57.51 REMARK 500 PHE A 179 -80.77 -159.42 REMARK 500 ASP A 182 -82.59 -133.61 REMARK 500 CYS A 191 -73.20 -58.90 REMARK 500 TYR A 223 146.69 -176.85 REMARK 500 ASP A 264 4.07 -56.23 REMARK 500 ARG A 289 43.12 -95.50 REMARK 500 ASN A 299 -10.40 61.65 REMARK 500 SER B 62 108.04 -10.05 REMARK 500 SER B 64 165.21 -42.46 REMARK 500 LYS B 71 -38.79 -38.25 REMARK 500 THR B 78 125.39 -27.92 REMARK 500 ASN B 79 71.80 30.37 REMARK 500 GLU B 107 -62.59 -103.48 REMARK 500 ARG B 108 -27.14 -23.48 REMARK 500 ALA B 112 97.92 -59.35 REMARK 500 ILE B 126 -6.85 -51.45 REMARK 500 CYS B 141 7.27 58.16 REMARK 500 PHE B 179 -91.03 -124.17 REMARK 500 ASP B 182 -106.59 -138.76 REMARK 500 ASN B 230 72.39 54.40 REMARK 500 PRO B 234 154.15 -44.28 REMARK 500 ASN B 259 96.52 -65.03 REMARK 500 LYS B 270 9.20 -65.43 REMARK 500 ASP B 276 -47.52 -29.11 REMARK 500 ALA B 288 34.83 -89.87 REMARK 500 VAL B 296 -36.29 -140.53 REMARK 500 ALA B 301 -138.71 -116.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 115 ASP A 116 -140.25 REMARK 500 LEU A 119 CYS A 120 -140.18 REMARK 500 ALA A 122 LYS A 123 -141.49 REMARK 500 LYS B 118 LEU B 119 149.80 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 TYR B 202 0.09 SIDE CHAIN REMARK 500 GLU B 253 0.12 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 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 174 OE1 REMARK 620 2 ASN A 180 OD1 78.3 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GKP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ENDOG WORM HOMOLOGUE CPS-6 H148A/F122A IN REMARK 900 COMPLEX WITH DNA DBREF 9M1E A 63 305 UNP Q95NM6 NUCG_CAEEL 63 305 DBREF 9M1E B 63 305 UNP Q95NM6 NUCG_CAEEL 63 305 SEQADV 9M1E MET A 54 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E HIS A 55 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E HIS A 56 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E HIS A 57 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E HIS A 58 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E HIS A 59 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E HIS A 60 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E GLY A 61 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E SER A 62 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E ALA A 122 UNP Q95NM6 PHE 122 ENGINEERED MUTATION SEQADV 9M1E ALA A 148 UNP Q95NM6 HIS 148 ENGINEERED MUTATION SEQADV 9M1E MET B 54 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E HIS B 55 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E HIS B 56 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E HIS B 57 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E HIS B 58 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E HIS B 59 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E HIS B 60 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E GLY B 61 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E SER B 62 UNP Q95NM6 EXPRESSION TAG SEQADV 9M1E ALA B 122 UNP Q95NM6 PHE 122 ENGINEERED MUTATION SEQADV 9M1E ALA B 148 UNP Q95NM6 HIS 148 ENGINEERED MUTATION SEQRES 1 A 252 MET HIS HIS HIS HIS HIS HIS GLY SER PRO SER ARG SER SEQRES 2 A 252 ALA GLU ILE MET LYS HIS GLY TYR PRO GLY PHE THR ASN SEQRES 3 A 252 VAL ARG THR TYR GLU ASP PHE VAL LEU SER TYR ASP TYR SEQRES 4 A 252 LYS THR ARG THR ALA HIS TRP VAL CYS GLU HIS LEU THR SEQRES 5 A 252 PRO GLU ARG LEU LYS HIS ALA GLU GLY VAL ASP ARG LYS SEQRES 6 A 252 LEU CYS GLU ALA LYS PRO ASP ILE THR PHE PRO GLN LYS SEQRES 7 A 252 PHE LEU SER GLN ASN THR ASP TYR LYS CYS SER GLY PHE SEQRES 8 A 252 ASP ARG GLY ALA LEU ALA ALA ALA GLY ASN HIS ARG LYS SEQRES 9 A 252 SER GLN LEU ALA VAL ASP GLN THR PHE TYR LEU SER ASN SEQRES 10 A 252 MET SER PRO GLN VAL GLY ARG GLY PHE ASN ARG ASP LYS SEQRES 11 A 252 TRP ASN ASP LEU GLU MET HIS CYS ARG ARG VAL ALA LYS SEQRES 12 A 252 LYS MET ILE ASN SER TYR ILE ILE THR GLY PRO LEU TYR SEQRES 13 A 252 LEU PRO LYS LEU GLU GLY ASP GLY LYS LYS TYR ILE LYS SEQRES 14 A 252 TYR GLN VAL ILE GLY ASP ASN ASN VAL ALA VAL PRO THR SEQRES 15 A 252 HIS PHE PHE LYS VAL ALA LEU PHE GLU VAL THR PRO GLY SEQRES 16 A 252 LYS PHE GLU LEU GLU SER TYR ILE LEU PRO ASN ALA VAL SEQRES 17 A 252 ILE GLU ASP THR VAL GLU ILE SER LYS PHE HIS VAL PRO SEQRES 18 A 252 LEU ASP ALA VAL GLU ARG SER ALA GLY LEU GLU ILE PHE SEQRES 19 A 252 ALA ARG LEU ASP PRO LYS SER ILE VAL LYS GLU ASN GLY SEQRES 20 A 252 ALA LYS LYS GLY GLY SEQRES 1 B 252 MET HIS HIS HIS HIS HIS HIS GLY SER PRO SER ARG SER SEQRES 2 B 252 ALA GLU ILE MET LYS HIS GLY TYR PRO GLY PHE THR ASN SEQRES 3 B 252 VAL ARG THR TYR GLU ASP PHE VAL LEU SER TYR ASP TYR SEQRES 4 B 252 LYS THR ARG THR ALA HIS TRP VAL CYS GLU HIS LEU THR SEQRES 5 B 252 PRO GLU ARG LEU LYS HIS ALA GLU GLY VAL ASP ARG LYS SEQRES 6 B 252 LEU CYS GLU ALA LYS PRO ASP ILE THR PHE PRO GLN LYS SEQRES 7 B 252 PHE LEU SER GLN ASN THR ASP TYR LYS CYS SER GLY PHE SEQRES 8 B 252 ASP ARG GLY ALA LEU ALA ALA ALA GLY ASN HIS ARG LYS SEQRES 9 B 252 SER GLN LEU ALA VAL ASP GLN THR PHE TYR LEU SER ASN SEQRES 10 B 252 MET SER PRO GLN VAL GLY ARG GLY PHE ASN ARG ASP LYS SEQRES 11 B 252 TRP ASN ASP LEU GLU MET HIS CYS ARG ARG VAL ALA LYS SEQRES 12 B 252 LYS MET ILE ASN SER TYR ILE ILE THR GLY PRO LEU TYR SEQRES 13 B 252 LEU PRO LYS LEU GLU GLY ASP GLY LYS LYS TYR ILE LYS SEQRES 14 B 252 TYR GLN VAL ILE GLY ASP ASN ASN VAL ALA VAL PRO THR SEQRES 15 B 252 HIS PHE PHE LYS VAL ALA LEU PHE GLU VAL THR PRO GLY SEQRES 16 B 252 LYS PHE GLU LEU GLU SER TYR ILE LEU PRO ASN ALA VAL SEQRES 17 B 252 ILE GLU ASP THR VAL GLU ILE SER LYS PHE HIS VAL PRO SEQRES 18 B 252 LEU ASP ALA VAL GLU ARG SER ALA GLY LEU GLU ILE PHE SEQRES 19 B 252 ALA ARG LEU ASP PRO LYS SER ILE VAL LYS GLU ASN GLY SEQRES 20 B 252 ALA LYS LYS GLY GLY HET STL A 401 29 HET STL A 402 29 HET MG A 403 1 HET STL B 401 29 HET STL B 402 29 HET MG B 403 1 HETNAM STL RESVERATROL HETNAM MG MAGNESIUM ION FORMUL 3 STL 4(C14 H12 O3) FORMUL 5 MG 2(MG 2+) FORMUL 9 HOH *4(H2 O) HELIX 1 AA1 SER A 64 MET A 70 1 7 HELIX 2 AA2 LYS A 71 GLY A 73 5 3 HELIX 3 AA3 GLN A 135 LYS A 140 1 6 HELIX 4 AA4 ALA A 151 HIS A 155 5 5 HELIX 5 AA5 SER A 158 GLN A 164 1 7 HELIX 6 AA6 THR A 165 SER A 169 5 5 HELIX 7 AA7 ASP A 182 LYS A 196 1 15 HELIX 8 AA8 GLU A 267 HIS A 272 5 6 HELIX 9 AA9 PRO A 274 GLY A 283 1 10 HELIX 10 AB1 ASP A 291 LYS A 293 5 3 HELIX 11 AB2 SER B 64 MET B 70 1 7 HELIX 12 AB3 ASP B 116 CYS B 120 5 5 HELIX 13 AB4 PRO B 129 LEU B 133 5 5 HELIX 14 AB5 GLN B 135 LYS B 140 1 6 HELIX 15 AB6 ALA B 151 HIS B 155 5 5 HELIX 16 AB7 SER B 158 PHE B 166 1 9 HELIX 17 AB8 TYR B 167 SER B 169 5 3 HELIX 18 AB9 ASP B 182 LYS B 196 1 15 HELIX 19 AC1 ILE B 268 HIS B 272 5 5 HELIX 20 AC2 PRO B 274 GLY B 283 1 10 HELIX 21 AC3 ASP B 291 LYS B 293 5 3 SHEET 1 AA1 8 VAL A 80 THR A 82 0 SHEET 2 AA1 8 VAL A 87 ASP A 91 -1 O LEU A 88 N ARG A 81 SHEET 3 AA1 8 THR A 96 LEU A 104 -1 O THR A 96 N ASP A 91 SHEET 4 AA1 8 ASN A 200 LEU A 208 -1 O SER A 201 N LEU A 104 SHEET 5 AA1 8 HIS A 236 THR A 246 -1 O GLU A 244 N ASN A 200 SHEET 6 AA1 8 LYS A 249 PRO A 258 -1 O LEU A 257 N PHE A 237 SHEET 7 AA1 8 ILE A 295 GLU A 298 1 O LYS A 297 N LEU A 252 SHEET 8 AA1 8 ALA A 301 LYS A 302 -1 O ALA A 301 N GLU A 298 SHEET 1 AA2 2 PHE A 144 ALA A 148 0 SHEET 2 AA2 2 MET A 171 VAL A 175 -1 O SER A 172 N GLY A 147 SHEET 1 AA3 4 LYS A 212 LEU A 213 0 SHEET 2 AA3 4 LYS A 219 ILE A 226 -1 O TYR A 220 N LYS A 212 SHEET 3 AA3 4 LYS B 219 ILE B 226 -1 O ILE B 221 N TYR A 223 SHEET 4 AA3 4 LYS B 212 LEU B 213 -1 N LYS B 212 O TYR B 220 SHEET 1 AA4 4 VAL A 231 ALA A 232 0 SHEET 2 AA4 4 LYS A 219 ILE A 226 -1 N ILE A 226 O VAL A 231 SHEET 3 AA4 4 LYS B 219 ILE B 226 -1 O ILE B 221 N TYR A 223 SHEET 4 AA4 4 VAL B 231 ALA B 232 -1 O VAL B 231 N ILE B 226 SHEET 1 AA5 7 VAL B 80 THR B 82 0 SHEET 2 AA5 7 VAL B 87 TYR B 90 -1 O LEU B 88 N ARG B 81 SHEET 3 AA5 7 ALA B 97 LEU B 104 -1 O HIS B 98 N SER B 89 SHEET 4 AA5 7 ASN B 200 LEU B 208 -1 O SER B 201 N LEU B 104 SHEET 5 AA5 7 HIS B 236 THR B 246 -1 O LEU B 242 N TYR B 202 SHEET 6 AA5 7 LYS B 249 PRO B 258 -1 O GLU B 251 N PHE B 243 SHEET 7 AA5 7 ILE B 295 GLU B 298 1 O VAL B 296 N PHE B 250 SHEET 1 AA6 2 ASP B 145 ALA B 148 0 SHEET 2 AA6 2 MET B 171 GLN B 174 -1 O SER B 172 N GLY B 147 LINK OE1 GLN A 174 MG MG A 403 1555 1555 2.83 LINK OD1 ASN A 180 MG MG A 403 1555 1555 2.35 LINK OD1 ASN B 180 MG MG B 403 1555 1555 2.82 CRYST1 71.661 45.856 81.003 90.00 102.81 90.00 P 1 21 1 4 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 0.013955 0.000000 0.003173 0.00000 SCALE2 0.000000 0.021807 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012660 0.00000 CONECT 1629 7658 CONECT 1719 7658 CONECT 5611 7717 CONECT 7600 7601 7605 7616 CONECT 7601 7600 7602 7617 CONECT 7602 7601 7603 7615 CONECT 7603 7602 7604 7618 CONECT 7604 7603 7605 7606 CONECT 7605 7600 7604 7619 CONECT 7606 7604 7607 7620 CONECT 7607 7606 7608 7621 CONECT 7608 7607 7609 7613 CONECT 7609 7608 7610 7622 CONECT 7610 7609 7611 7623 CONECT 7611 7610 7612 7614 CONECT 7612 7611 7613 7624 CONECT 7613 7608 7612 7625 CONECT 7614 7611 7626 CONECT 7615 7602 7627 CONECT 7616 7600 7628 CONECT 7617 7601 CONECT 7618 7603 CONECT 7619 7605 CONECT 7620 7606 CONECT 7621 7607 CONECT 7622 7609 CONECT 7623 7610 CONECT 7624 7612 CONECT 7625 7613 CONECT 7626 7614 CONECT 7627 7615 CONECT 7628 7616 CONECT 7629 7630 7634 7645 CONECT 7630 7629 7631 7646 CONECT 7631 7630 7632 7644 CONECT 7632 7631 7633 7647 CONECT 7633 7632 7634 7635 CONECT 7634 7629 7633 7648 CONECT 7635 7633 7636 7649 CONECT 7636 7635 7637 7650 CONECT 7637 7636 7638 7642 CONECT 7638 7637 7639 7651 CONECT 7639 7638 7640 7652 CONECT 7640 7639 7641 7643 CONECT 7641 7640 7642 7653 CONECT 7642 7637 7641 7654 CONECT 7643 7640 7655 CONECT 7644 7631 7656 CONECT 7645 7629 7657 CONECT 7646 7630 CONECT 7647 7632 CONECT 7648 7634 CONECT 7649 7635 CONECT 7650 7636 CONECT 7651 7638 CONECT 7652 7639 CONECT 7653 7641 CONECT 7654 7642 CONECT 7655 7643 CONECT 7656 7644 CONECT 7657 7645 CONECT 7658 1629 1719 CONECT 7659 7660 7664 7675 CONECT 7660 7659 7661 7676 CONECT 7661 7660 7662 7674 CONECT 7662 7661 7663 7677 CONECT 7663 7662 7664 7665 CONECT 7664 7659 7663 7678 CONECT 7665 7663 7666 7679 CONECT 7666 7665 7667 7680 CONECT 7667 7666 7668 7672 CONECT 7668 7667 7669 7681 CONECT 7669 7668 7670 7682 CONECT 7670 7669 7671 7673 CONECT 7671 7670 7672 7683 CONECT 7672 7667 7671 7684 CONECT 7673 7670 7685 CONECT 7674 7661 7686 CONECT 7675 7659 7687 CONECT 7676 7660 CONECT 7677 7662 CONECT 7678 7664 CONECT 7679 7665 CONECT 7680 7666 CONECT 7681 7668 CONECT 7682 7669 CONECT 7683 7671 CONECT 7684 7672 CONECT 7685 7673 CONECT 7686 7674 CONECT 7687 7675 CONECT 7688 7689 7693 7704 CONECT 7689 7688 7690 7705 CONECT 7690 7689 7691 7703 CONECT 7691 7690 7692 7706 CONECT 7692 7691 7693 7694 CONECT 7693 7688 7692 7707 CONECT 7694 7692 7695 7708 CONECT 7695 7694 7696 7709 CONECT 7696 7695 7697 7701 CONECT 7697 7696 7698 7710 CONECT 7698 7697 7699 7711 CONECT 7699 7698 7700 7702 CONECT 7700 7699 7701 7712 CONECT 7701 7696 7700 7713 CONECT 7702 7699 7714 CONECT 7703 7690 7715 CONECT 7704 7688 7716 CONECT 7705 7689 CONECT 7706 7691 CONECT 7707 7693 CONECT 7708 7694 CONECT 7709 7695 CONECT 7710 7697 CONECT 7711 7698 CONECT 7712 7700 CONECT 7713 7701 CONECT 7714 7702 CONECT 7715 7703 CONECT 7716 7704 CONECT 7717 5611 MASTER 402 0 6 21 27 0 0 6 3898 2 121 40 END