10 20 30 40 50 60 70 80 5GKP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE/DNA 05-JUL-16 5GKP
TITLE CRYSTAL STRUCTURE OF THE ENDOG WORM HOMOLOGUE CPS-6 H148A/F122A IN TITLE 2 COMPLEX WITH DNA
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 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*TP*TP*TP*TP*T)-3'); COMPND 11 CHAIN: C, D; COMPND 12 ENGINEERED: YES
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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32644
KEYWDS ENDOG, MITOCHONDRIA, ENDONUCLEASE, NON-SPECIFIC NUCLEASE, PROTEIN-DNA KEYWDS 2 INTERACTIONS, HYDROLASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR J.L.LIN,H.S.YUAN
REVDAT 1 23-NOV-16 5GKP 0
JRNL AUTH J.L.LIN,C.C.WU,W.Z.YANG,H.S.YUAN JRNL TITL CRYSTAL STRUCTURE OF ENDONUCLEASE G IN COMPLEX WITH DNA JRNL TITL 2 REVEALS HOW IT NONSPECIFICALLY DEGRADES DNA AS A HOMODIMER. JRNL REF NUCLEIC ACIDS RES. 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27738134 JRNL DOI 10.1093/NAR/GKW931
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.L.LIN,H.S.YUAN REMARK 1 TITL STRUCTURALINSIGHTSINTOAPOPTOTICDNADEGRADATIONBYCED-3 REMARK 1 TITL 2 PROTEASESUPPRESSOR-6(CPS-6)FROMCAENORHABDITISELEGANS REMARK 1 REF J.BIOL.CHEM. V. 287 7110 2012 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 22223640 REMARK 1 DOI 10.1074/JBC.M111.316075
REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 24707 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.260 REMARK 3 FREE R VALUE TEST SET COUNT : 2042 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 19.7836 - 5.5527 0.70 2023 185 0.1859 0.2369 REMARK 3 2 5.5527 - 4.4235 0.56 1612 147 0.1390 0.2072 REMARK 3 3 4.4235 - 3.8691 0.54 1556 140 0.1433 0.2176 REMARK 3 4 3.8691 - 3.5175 0.54 1551 139 0.1674 0.2622 REMARK 3 5 3.5175 - 3.2666 0.53 1538 138 0.1680 0.2572 REMARK 3 6 3.2666 - 3.0748 0.53 1532 139 0.1956 0.2793 REMARK 3 7 3.0748 - 2.9213 0.53 1521 136 0.1906 0.2430 REMARK 3 8 2.9213 - 2.7945 0.53 1522 137 0.1884 0.2646 REMARK 3 9 2.7945 - 2.6872 0.53 1503 135 0.1890 0.3114 REMARK 3 10 2.6872 - 2.5947 0.53 1538 139 0.1951 0.2786 REMARK 3 11 2.5947 - 2.5137 0.53 1516 135 0.1852 0.2731 REMARK 3 12 2.5137 - 2.4420 0.52 1498 135 0.1869 0.2922 REMARK 3 13 2.4420 - 2.3778 0.50 1437 129 0.1904 0.3234 REMARK 3 14 2.3778 - 2.3199 0.44 1250 112 0.2053 0.2799 REMARK 3 15 2.3199 - 2.2700 0.37 1068 96 0.2074 0.2411 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.014 4104 REMARK 3 ANGLE : 1.426 5578 REMARK 3 CHIRALITY : 0.058 600 REMARK 3 PLANARITY : 0.007 688 REMARK 3 DIHEDRAL : 16.849 1547 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: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 I_PLUS/MINUS COLUMNS
REMARK 4 REMARK 4 5GKP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1300000955.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JAN-14 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 : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : LN2-COOLED FIXED-EXIT DOUBLE REMARK 200 CRYSTAL SI(111) MONOCHROMATOR REMARK 200 OPTICS : VERTICALLY COLLIMATING REMARK 200 PREMIRROR, LN2-COOLED FIXED-EXIT REMARK 200 DOUBLE CRYSTAL SI(111) REMARK 200 MONOCHROMATOR, TOROIDAL FOCUSING REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25101 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3S5B REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 30% PEG 1000, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 279K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 28.33600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.95700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.28100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.95700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.33600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.28100 REMARK 290 SMTRY3 4 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: 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 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 PRO A 63 REMARK 465 HIS A 111 REMARK 465 ALA A 112 REMARK 465 GLU A 113 REMARK 465 LYS A 302 REMARK 465 LYS A 303 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 HIS B 60 REMARK 465 GLY B 61 REMARK 465 SER B 62 REMARK 465 ASP B 264 REMARK 465 LYS B 303 REMARK 465 GLY B 304 REMARK 465 GLY B 305 REMARK 465 DT C 2 REMARK 465 DG C 3 REMARK 465 DT C 4 REMARK 465 DT D 2 REMARK 465 DG D 3 REMARK 465 DT D 4
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 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 C ASP B 216 H GLY B 217 1.34 REMARK 500 H PHE A 287 O HOH A 502 1.55 REMARK 500 HH TYR A 202 O HOH A 501 1.59 REMARK 500 NH1 ARG B 117 OP2 DT D -2 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT D -3 C5' DT D -3 C4' 0.051 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 ASP B 216 N - CA - C ANGL. DEV. = -17.2 DEGREES REMARK 500 GLY B 217 C - N - CA ANGL. DEV. = 13.0 DEGREES REMARK 500 DT C 1 O4' - C1' - N1 ANGL. DEV. = 2.6 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 PHE A 179 -90.26 -142.24 REMARK 500 ASP A 182 -96.66 -132.07 REMARK 500 ASP B 116 135.24 -177.43 REMARK 500 LEU B 119 39.92 -92.79 REMARK 500 PHE B 179 -87.70 -144.89 REMARK 500 ASP B 182 -108.30 -139.52 REMARK 500 ASP B 216 -107.91 -124.85 REMARK 500 ARG B 289 38.16 -71.51 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 GLY B 215 ASP B 216 147.67 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 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 180 OD1 REMARK 620 2 DT C -2 O3' 95.9 REMARK 620 3 DT C -1 OP1 103.4 56.1 REMARK 620 4 HOH A 505 O 167.2 93.9 88.9 REMARK 620 5 HOH A 530 O 74.4 82.8 138.7 98.9 REMARK 620 6 HOH A 532 O 89.1 161.1 105.1 84.1 116.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 180 OD1 REMARK 620 2 DT D -2 O3' 103.9 REMARK 620 3 DT D -1 OP1 102.5 57.0 REMARK 620 4 HOH B 516 O 86.1 161.5 106.1 REMARK 620 5 HOH B 566 O 77.8 88.8 145.2 108.7 REMARK 620 6 HOH B 513 O 162.1 90.7 94.1 82.8 92.5 REMARK 620 N 1 2 3 4 5
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 401
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GKC RELATED DB: PDB
DBREF 5GKP A 63 305 UNP Q95NM6 NUCG_CAEEL 63 305 DBREF 5GKP B 63 305 UNP Q95NM6 NUCG_CAEEL 63 305 DBREF 5GKP C -3 4 PDB 5GKP 5GKP -3 4 DBREF 5GKP D -3 4 PDB 5GKP 5GKP -3 4
SEQADV 5GKP MET A 54 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP HIS A 55 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP HIS A 56 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP HIS A 57 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP HIS A 58 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP HIS A 59 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP HIS A 60 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP GLY A 61 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP SER A 62 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP ALA A 122 UNP Q95NM6 PHE 122 ENGINEERED MUTATION SEQADV 5GKP ALA A 148 UNP Q95NM6 HIS 148 ENGINEERED MUTATION SEQADV 5GKP MET B 54 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP HIS B 55 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP HIS B 56 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP HIS B 57 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP HIS B 58 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP HIS B 59 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP HIS B 60 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP GLY B 61 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP SER B 62 UNP Q95NM6 EXPRESSION TAG SEQADV 5GKP ALA B 122 UNP Q95NM6 PHE 122 ENGINEERED MUTATION SEQADV 5GKP 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 SEQRES 1 C 8 DT DT DT DT DT DT DG DT SEQRES 1 D 8 DT DT DT DT DT DT DG DT
HET MG A 401 1 HET MG B 401 1
HETNAM MG MAGNESIUM ION
FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *175(H2 O)
HELIX 1 AA1 SER A 64 MET A 70 1 7 HELIX 2 AA2 PRO A 129 LEU A 133 5 5 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 THR A 165 1 8 HELIX 6 AA6 PHE A 166 SER A 169 5 4 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 PRO B 106 LYS B 110 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 GLN B 164 1 7 HELIX 17 AB8 THR B 165 SER B 169 5 5 HELIX 18 AB9 ASP B 182 LYS B 196 1 15 HELIX 19 AC1 GLU B 267 HIS B 272 5 6 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 7 VAL A 80 THR A 82 0 SHEET 2 AA1 7 PHE A 86 ASP A 91 -1 O LEU A 88 N ARG A 81 SHEET 3 AA1 7 THR A 96 LEU A 104 -1 O HIS A 98 N SER A 89 SHEET 4 AA1 7 SER A 201 LEU A 208 -1 O SER A 201 N LEU A 104 SHEET 5 AA1 7 HIS A 236 GLU A 244 -1 O LEU A 242 N TYR A 202 SHEET 6 AA1 7 PHE A 250 PRO A 258 -1 O GLU A 251 N PHE A 243 SHEET 7 AA1 7 ILE A 295 GLU A 298 1 O LYS A 297 N LEU A 252 SHEET 1 AA2 2 ASP A 145 ALA A 148 0 SHEET 2 AA2 2 MET A 171 GLN A 174 -1 O GLN A 174 N ASP A 145 SHEET 1 AA3 4 PRO A 211 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 TYR B 223 N ILE A 221 SHEET 4 AA3 4 PRO B 211 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 TYR B 223 N ILE A 221 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 ASP B 91 -1 O LEU B 88 N ARG B 81 SHEET 3 AA5 7 THR B 96 LEU B 104 -1 O TRP B 99 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 GLU B 244 N ASN B 200 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 LYS B 297 N LEU B 252 SHEET 1 AA6 2 ASP B 145 ALA B 148 0 SHEET 2 AA6 2 MET B 171 GLN B 174 -1 O GLN B 174 N ASP B 145
LINK OD1 ASN A 180 MG MG A 401 1555 1555 2.25 LINK OD1 ASN B 180 MG MG B 401 1555 1555 2.32 LINK O3' DT C -2 MG MG A 401 1555 1555 2.79 LINK OP1 DT C -1 MG MG A 401 1555 1555 2.44 LINK O3' DT D -2 MG MG B 401 1555 1555 2.74 LINK OP1 DT D -1 MG MG B 401 1555 1555 2.32 LINK MG MG A 401 O HOH A 505 1555 1555 2.35 LINK MG MG A 401 O HOH A 530 1555 1555 2.47 LINK MG MG A 401 O HOH A 532 1555 1555 2.22 LINK MG MG B 401 O HOH B 516 1555 1555 2.22 LINK MG MG B 401 O HOH B 566 1555 1555 2.42 LINK MG MG B 401 O HOH B 513 1555 1555 2.41
SITE 1 AC1 6 ASN A 180 HOH A 505 HOH A 530 HOH A 532 SITE 2 AC1 6 DT C -1 DT C -2 SITE 1 AC2 6 ASN B 180 HOH B 513 HOH B 516 HOH B 566 SITE 2 AC2 6 DT D -2 DT D -1
CRYST1 56.672 72.562 127.914 90.00 90.00 90.00 P 21 21 21 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 0.017645 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013781 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007818 0.00000