PDB Short entry for 5GKI HEADER HYDROLASE/DNA 04-JUL-16 5GKI TITLE STRUCTURE OF ENDOMS-DSDNA3 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE ENDOMS; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ENDONUCLEASE NUCS; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*CP*CP*TP*AP*GP*GP*TP*CP*CP*CP*GP*TP*CP*C)- COMPND 10 3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*GP*GP*AP*CP*GP*GP*GP*GP*CP*CP*TP*AP*GP*GP*C)- COMPND 15 3'); COMPND 16 CHAIN: D; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS KOD1; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 GENE: TK1898; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS ENDONUCLEASE, DNA COMPLEX, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.NAKAE,A.HIJIKATA,T.TSUJI,K.YONEZAWA,K.KOUYAMA,K.MAYANAGI,S.ISHINO, AUTHOR 2 Y.ISHINO,T.SHIRAI REVDAT 4 08-NOV-23 5GKI 1 LINK REVDAT 3 26-FEB-20 5GKI 1 JRNL REMARK REVDAT 2 16-NOV-16 5GKI 1 JRNL REVDAT 1 02-NOV-16 5GKI 0 JRNL AUTH S.NAKAE,A.HIJIKATA,T.TSUJI,K.YONEZAWA,K.I.KOUYAMA, JRNL AUTH 2 K.MAYANAGI,S.ISHINO,Y.ISHINO,T.SHIRAI JRNL TITL STRUCTURE OF THE ENDOMS-DNA COMPLEX AS MISMATCH RESTRICTION JRNL TITL 2 ENDONUCLEASE JRNL REF STRUCTURE V. 24 1960 2016 JRNL REFN ISSN 0969-2126 JRNL PMID 27773688 JRNL DOI 10.1016/J.STR.2016.09.005 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 22831 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1162 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 24.7247 - 5.7784 0.99 3045 138 0.1957 0.2612 REMARK 3 2 5.7784 - 4.5961 0.99 2834 143 0.1482 0.2179 REMARK 3 3 4.5961 - 4.0179 0.99 2776 158 0.1313 0.1881 REMARK 3 4 4.0179 - 3.6518 0.98 2705 159 0.1569 0.2176 REMARK 3 5 3.6518 - 3.3908 0.97 2658 163 0.1700 0.2746 REMARK 3 6 3.3908 - 3.1913 0.96 2634 131 0.2039 0.2765 REMARK 3 7 3.1913 - 3.0318 0.93 2550 145 0.2567 0.3214 REMARK 3 8 3.0318 - 2.9000 0.91 2467 125 0.3296 0.4544 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.38 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 : 0.009 5252 REMARK 3 ANGLE : 1.281 7340 REMARK 3 CHIRALITY : 0.046 834 REMARK 3 PLANARITY : 0.007 734 REMARK 3 DIHEDRAL : 22.406 2120 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 5GKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1300000899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-14 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 : 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) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : MOSFLM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23761 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 24.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.200 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: 5BSL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.16 M CALCIUM ACETATE, 80 MM SODIUM REMARK 280 CACODYLATE, 14.4%(W/V) PEG8000, 20%(W/V) GLYCEROL, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 135.11667 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 270.23333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 202.67500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 337.79167 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 67.55833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 135.11667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 270.23333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 337.79167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 202.67500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 67.55833 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 TOTAL BURIED SURFACE AREA: 13560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -123.0 KCAL/MOL 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 1 REMARK 465 ASP A 241 REMARK 465 SER A 242 REMARK 465 LYS A 243 REMARK 465 LYS A 244 REMARK 465 LYS A 245 REMARK 465 GLY A 246 REMARK 465 ARG A 247 REMARK 465 GLN A 248 REMARK 465 LYS A 249 REMARK 465 THR A 250 REMARK 465 LEU A 251 REMARK 465 PHE A 252 REMARK 465 MET B 1 REMARK 465 ASP B 241 REMARK 465 SER B 242 REMARK 465 LYS B 243 REMARK 465 LYS B 244 REMARK 465 LYS B 245 REMARK 465 GLY B 246 REMARK 465 ARG B 247 REMARK 465 GLN B 248 REMARK 465 LYS B 249 REMARK 465 THR B 250 REMARK 465 LEU B 251 REMARK 465 PHE B 252 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 DA C 5 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA C 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT C 13 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG D 5 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG D 5 O4' - C1' - N9 ANGL. DEV. = 2.1 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 3 -157.41 -155.34 REMARK 500 ALA A 45 -169.23 -126.67 REMARK 500 LYS A 71 -165.77 56.99 REMARK 500 LYS A 100 78.45 51.75 REMARK 500 ILE A 146 -62.88 -91.48 REMARK 500 LEU A 153 -57.64 -123.43 REMARK 500 SER B 11 62.00 32.11 REMARK 500 LYS B 71 -159.96 52.43 REMARK 500 ARG B 72 -55.71 -122.84 REMARK 500 LYS B 100 66.79 63.32 REMARK 500 LEU B 153 -58.10 -123.42 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 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 179 OE1 REMARK 620 2 GLU A 179 OE2 52.4 REMARK 620 3 DG C 6 OP1 82.2 134.4 REMARK 620 4 DG D 6 OP1 82.7 135.1 3.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 179 OE1 REMARK 620 2 GLU B 179 OE2 61.4 REMARK 620 3 DG C 6 OP1 76.9 97.8 REMARK 620 4 DG D 6 OP1 76.8 102.4 5.6 REMARK 620 N 1 2 3 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD C 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GKE RELATED DB: PDB REMARK 900 RELATED ID: 5GKF RELATED DB: PDB REMARK 900 RELATED ID: 5GKG RELATED DB: PDB REMARK 900 RELATED ID: 5GKH RELATED DB: PDB REMARK 900 RELATED ID: 5GKJ RELATED DB: PDB DBREF 5GKI A 1 252 UNP Q5JER9 NUCS_THEKO 1 252 DBREF 5GKI B 1 252 UNP Q5JER9 NUCS_THEKO 1 252 DBREF 5GKI C 1 15 PDB 5GKI 5GKI 1 15 DBREF 5GKI D 1 15 PDB 5GKI 5GKI 1 15 SEQADV 5GKI ALA A 165 UNP Q5JER9 ASP 165 ENGINEERED MUTATION SEQADV 5GKI ALA B 165 UNP Q5JER9 ASP 165 ENGINEERED MUTATION SEQRES 1 A 252 MET SER LYS ASP LYS VAL THR VAL ILE THR SER PRO SER SEQRES 2 A 252 THR GLU GLU LEU VAL SER LEU VAL ASN SER ALA LEU LEU SEQRES 3 A 252 GLU GLU ALA MET LEU THR ILE PHE ALA ARG CYS LYS VAL SEQRES 4 A 252 HIS TYR ASP GLY ARG ALA LYS SER GLU LEU GLY SER GLY SEQRES 5 A 252 ASP ARG VAL ILE ILE VAL LYS PRO ASP GLY SER PHE LEU SEQRES 6 A 252 ILE HIS GLN SER LYS LYS ARG GLU PRO VAL ASN TRP GLN SEQRES 7 A 252 PRO PRO GLY SER ARG VAL ARG LEU GLU LEU ARG GLU ASN SEQRES 8 A 252 PRO VAL LEU VAL SER ILE ARG ARG LYS PRO ARG GLU THR SEQRES 9 A 252 LEU GLU VAL GLU LEU GLU GLU VAL TYR MET VAL SER VAL SEQRES 10 A 252 PHE ARG ALA GLU ASP TYR GLU GLU LEU ALA LEU THR GLY SEQRES 11 A 252 SER GLU ALA GLU MET ALA GLU LEU ILE PHE GLU ASN PRO SEQRES 12 A 252 GLU VAL ILE GLU PRO GLY PHE LYS PRO LEU PHE ARG GLU SEQRES 13 A 252 LYS ALA ILE GLY THR GLY ILE VAL ALA VAL LEU GLY ARG SEQRES 14 A 252 ASP SER ASP GLY ASN ILE VAL VAL LEU GLU LEU LYS ARG SEQRES 15 A 252 ARG ARG ALA GLU LEU HIS ALA VAL ARG GLN LEU LYS SER SEQRES 16 A 252 TYR VAL GLU ILE LEU ARG GLU GLU TYR GLY ASP LYS VAL SEQRES 17 A 252 ARG GLY ILE LEU VAL ALA PRO SER LEU THR SER GLY ALA SEQRES 18 A 252 LYS ARG LEU LEU GLU LYS GLU GLY LEU GLU PHE ARG LYS SEQRES 19 A 252 LEU GLU PRO PRO LYS ARG ASP SER LYS LYS LYS GLY ARG SEQRES 20 A 252 GLN LYS THR LEU PHE SEQRES 1 B 252 MET SER LYS ASP LYS VAL THR VAL ILE THR SER PRO SER SEQRES 2 B 252 THR GLU GLU LEU VAL SER LEU VAL ASN SER ALA LEU LEU SEQRES 3 B 252 GLU GLU ALA MET LEU THR ILE PHE ALA ARG CYS LYS VAL SEQRES 4 B 252 HIS TYR ASP GLY ARG ALA LYS SER GLU LEU GLY SER GLY SEQRES 5 B 252 ASP ARG VAL ILE ILE VAL LYS PRO ASP GLY SER PHE LEU SEQRES 6 B 252 ILE HIS GLN SER LYS LYS ARG GLU PRO VAL ASN TRP GLN SEQRES 7 B 252 PRO PRO GLY SER ARG VAL ARG LEU GLU LEU ARG GLU ASN SEQRES 8 B 252 PRO VAL LEU VAL SER ILE ARG ARG LYS PRO ARG GLU THR SEQRES 9 B 252 LEU GLU VAL GLU LEU GLU GLU VAL TYR MET VAL SER VAL SEQRES 10 B 252 PHE ARG ALA GLU ASP TYR GLU GLU LEU ALA LEU THR GLY SEQRES 11 B 252 SER GLU ALA GLU MET ALA GLU LEU ILE PHE GLU ASN PRO SEQRES 12 B 252 GLU VAL ILE GLU PRO GLY PHE LYS PRO LEU PHE ARG GLU SEQRES 13 B 252 LYS ALA ILE GLY THR GLY ILE VAL ALA VAL LEU GLY ARG SEQRES 14 B 252 ASP SER ASP GLY ASN ILE VAL VAL LEU GLU LEU LYS ARG SEQRES 15 B 252 ARG ARG ALA GLU LEU HIS ALA VAL ARG GLN LEU LYS SER SEQRES 16 B 252 TYR VAL GLU ILE LEU ARG GLU GLU TYR GLY ASP LYS VAL SEQRES 17 B 252 ARG GLY ILE LEU VAL ALA PRO SER LEU THR SER GLY ALA SEQRES 18 B 252 LYS ARG LEU LEU GLU LYS GLU GLY LEU GLU PHE ARG LYS SEQRES 19 B 252 LEU GLU PRO PRO LYS ARG ASP SER LYS LYS LYS GLY ARG SEQRES 20 B 252 GLN LYS THR LEU PHE SEQRES 1 C 15 DG DC DC DT DA DG DG DT DC DC DC DG DT SEQRES 2 C 15 DC DC SEQRES 1 D 15 DG DG DA DC DG DG DG DG DC DC DT DA DG SEQRES 2 D 15 DG DC HET MG A 301 1 HET MPD A 302 8 HET MG B 301 1 HET MPD C 101 8 HET MPD C 102 8 HET MPD C 103 8 HETNAM MG MAGNESIUM ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 5 MG 2(MG 2+) FORMUL 6 MPD 4(C6 H14 O2) FORMUL 11 HOH *21(H2 O) HELIX 1 AA1 SER A 13 GLU A 28 1 16 HELIX 2 AA2 SER A 131 ASN A 142 1 12 HELIX 3 AA3 PRO A 143 ILE A 146 5 4 HELIX 4 AA4 GLU A 186 GLY A 205 1 20 HELIX 5 AA5 THR A 218 GLU A 228 1 11 HELIX 6 AA6 SER B 13 GLU B 28 1 16 HELIX 7 AA7 SER B 131 ASN B 142 1 12 HELIX 8 AA8 PRO B 143 ILE B 146 5 4 HELIX 9 AA9 GLU B 186 GLY B 205 1 20 HELIX 10 AB1 ASP B 206 VAL B 208 5 3 HELIX 11 AB2 THR B 218 GLU B 228 1 11 SHEET 1 AA1 6 VAL A 6 THR A 10 0 SHEET 2 AA1 6 GLU A 103 PHE A 118 -1 O VAL A 115 N ILE A 9 SHEET 3 AA1 6 MET A 30 ASP A 42 -1 N ASP A 42 O THR A 104 SHEET 4 AA1 6 LYS A 46 VAL A 58 -1 O ILE A 56 N ILE A 33 SHEET 5 AA1 6 PRO A 92 ARG A 98 0 SHEET 6 AA1 6 ARG A 83 LEU A 88 -1 N ARG A 85 O VAL A 95 SHEET 1 AA2 6 ASN A 76 GLN A 78 0 SHEET 2 AA2 6 PHE A 64 HIS A 67 -1 N PHE A 64 O GLN A 78 SHEET 3 AA2 6 LYS A 46 VAL A 58 -1 N ILE A 57 O LEU A 65 SHEET 4 AA2 6 MET A 30 ASP A 42 -1 N ILE A 33 O ILE A 56 SHEET 5 AA2 6 GLU A 103 PHE A 118 -1 O THR A 104 N ASP A 42 SHEET 6 AA2 6 ALA B 127 THR B 129 0 SHEET 1 AA3 6 ALA A 127 THR A 129 0 SHEET 2 AA3 6 LYS B 46 VAL B 58 -1 O LYS B 46 N THR A 129 SHEET 3 AA3 6 MET B 30 ASP B 42 -1 N CYS B 37 O GLY B 52 SHEET 4 AA3 6 GLU B 103 PHE B 118 -1 O THR B 104 N ASP B 42 SHEET 5 AA3 6 PHE B 64 HIS B 67 0 SHEET 6 AA3 6 ASN B 76 GLN B 78 -1 O GLN B 78 N PHE B 64 SHEET 1 AA4 6 VAL B 6 THR B 10 0 SHEET 2 AA4 6 GLU B 103 PHE B 118 -1 O VAL B 115 N ILE B 9 SHEET 3 AA4 6 MET B 30 ASP B 42 -1 N ASP B 42 O THR B 104 SHEET 4 AA4 6 LYS B 46 VAL B 58 -1 O GLY B 52 N CYS B 37 SHEET 5 AA4 6 PRO B 92 ARG B 98 0 SHEET 6 AA4 6 ARG B 83 LEU B 88 -1 N ARG B 83 O ILE B 97 SHEET 1 AA5 5 LYS A 151 ALA A 158 0 SHEET 2 AA5 5 ILE A 163 ARG A 169 -1 O ARG A 169 N LYS A 151 SHEET 3 AA5 5 ILE A 175 LEU A 180 -1 O VAL A 176 N GLY A 168 SHEET 4 AA5 5 VAL A 208 ALA A 214 1 O VAL A 213 N GLU A 179 SHEET 5 AA5 5 GLU A 231 LYS A 234 1 O GLU A 231 N LEU A 212 SHEET 1 AA6 5 LYS B 151 ALA B 158 0 SHEET 2 AA6 5 ILE B 163 ARG B 169 -1 O ARG B 169 N LYS B 151 SHEET 3 AA6 5 ILE B 175 LEU B 180 -1 O VAL B 176 N GLY B 168 SHEET 4 AA6 5 ARG B 209 ALA B 214 1 O ILE B 211 N VAL B 177 SHEET 5 AA6 5 GLU B 231 LYS B 234 1 O GLU B 231 N LEU B 212 LINK OE1 GLU A 179 MG MG A 301 1555 1555 2.15 LINK OE2 GLU A 179 MG MG A 301 1555 1555 2.67 LINK MG MG A 301 OP1B DG C 6 1555 1555 2.03 LINK MG MG A 301 OP1A DG D 6 1555 1555 2.02 LINK OE1 GLU B 179 MG MG B 301 1555 1555 2.29 LINK OE2 GLU B 179 MG MG B 301 1555 1555 1.93 LINK MG MG B 301 OP1A DG C 6 1555 1555 2.17 LINK MG MG B 301 OP1B DG D 6 1555 1555 2.13 CISPEP 1 LYS A 100 PRO A 101 0 -3.79 CISPEP 2 LYS B 100 PRO B 101 0 -3.75 SITE 1 AC1 7 GLU A 179 LYS A 181 GLN A 192 DA C 5 SITE 2 AC1 7 DG C 6 DG D 5 DG D 6 SITE 1 AC2 4 THR A 10 SER A 11 GLU A 16 ASP B 172 SITE 1 AC3 6 GLU B 179 GLN B 192 DA C 5 DG C 6 SITE 2 AC3 6 DG D 5 DG D 6 SITE 1 AC4 10 TRP B 77 DG C 6 DG C 7 DT C 8 SITE 2 AC4 10 DC C 9 DC C 11 DG D 6 DG D 7 SITE 3 AC4 10 DG D 8 DC D 9 SITE 1 AC5 8 GLU A 156 DA C 5 DG C 6 DG C 12 SITE 2 AC5 8 DG D 5 DG D 6 DA D 12 DG D 13 SITE 1 AC6 8 GLU B 156 DA C 5 DG C 6 DG C 12 SITE 2 AC6 8 DT C 13 DG D 6 DA D 12 DG D 13 CRYST1 92.030 92.030 405.350 90.00 90.00 120.00 P 61 2 2 24 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 0.010866 0.006274 0.000000 0.00000 SCALE2 0.000000 0.012547 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002467 0.00000