HEADER TRANSFERASE 03-JUN-14 4UOG TITLE CRYSTALLOGRAPHIC STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM TITLE 2 LITOPENAEUS VANNAMEI COMPLEXED WITH DCDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 2.7.4.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LITOPENAEUS VANNAMEI; SOURCE 3 ORGANISM_COMMON: PACIFIC WHITE SHRIMP; SOURCE 4 ORGANISM_TAXID: 6689; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: SALT INDUCIBLE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PJEXPRESS414 KEYWDS TRANSFERASE, BINARY, COMPLEX, DCDP, PYRIMIDINE, BINDING SITE, KEYWDS 2 DESOXYNUCLEOTIDE EXPDTA X-RAY DIFFRACTION AUTHOR A.A.LOPEZ-ZAVALA,V.STOJANOFF,E.RUDINO-PINERA,R.R.SOTELO-MUNDO REVDAT 3 10-JAN-24 4UOG 1 REMARK LINK REVDAT 2 17-SEP-14 4UOG 1 JRNL REVDAT 1 10-SEP-14 4UOG 0 JRNL AUTH A.A.LOPEZ-ZAVALA,I.E.QUINTERO-REYES,J.S.CARRASCO-MIRANDA, JRNL AUTH 2 V.STOJANOFF,A.WEICHSEL,E.RUDINO-PINERA,R.R.SOTELO-MUNDO JRNL TITL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM PACIFIC JRNL TITL 2 SHRIMP (LITOPENAEUS VANNAMEI) IN BINARY COMPLEXES WITH JRNL TITL 3 PURINE AND PYRIMIDINE NUCLEOSIDE DIPHOSPHATES JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 79 1150 2014 JRNL REFN ESSN 1744-3091 JRNL PMID 25195883 JRNL DOI 10.1107/S2053230X1401557X REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 21497 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1099 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 19.3045 - 4.5825 1.00 2809 134 0.1437 0.2072 REMARK 3 2 4.5825 - 3.6453 0.98 2308 127 0.1389 0.2059 REMARK 3 3 3.6453 - 3.1868 0.99 2238 140 0.1716 0.2440 REMARK 3 4 3.1868 - 2.8965 0.99 2655 136 0.1976 0.2665 REMARK 3 5 2.8965 - 2.6895 0.99 2612 132 0.2189 0.3100 REMARK 3 6 2.6895 - 2.5313 0.99 2590 154 0.2330 0.2842 REMARK 3 7 2.5313 - 2.4048 0.98 2581 144 0.2576 0.3118 REMARK 3 8 2.4048 - 2.3002 0.98 2605 132 0.2835 0.3585 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : 25.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.80 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 3732 REMARK 3 ANGLE : 1.189 5046 REMARK 3 CHIRALITY : 0.049 534 REMARK 3 PLANARITY : 0.006 633 REMARK 3 DIHEDRAL : 13.408 1401 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4UOG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1290060863. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL CUT REMARK 200 OPTICS : TOROIDAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21500 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 19.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.30 REMARK 200 R MERGE FOR SHELL (I) : 0.70000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 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: PDB ENTRY 4UOF REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M TRIS-HCL REMARK 280 PH 8.5 AND 30% (V/V) 2-PROPANOL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.41000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.41000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.08000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 67.68500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.08000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 67.68500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 52.41000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.08000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 67.68500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.41000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.08000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 67.68500 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 20950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -163.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 52.41000 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 MET C 1 CG SD CE 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 O GLU B 151 O HOH A 2075 1.93 REMARK 500 OE1 GLU C 146 O HOH C 2037 1.93 REMARK 500 OD1 ASP C 45 O HOH C 2047 2.01 REMARK 500 NZ LYS B 11 O HOH B 2014 2.01 REMARK 500 NH2 ARG B 3 O HOH B 2005 2.03 REMARK 500 O HOH C 2059 O HOH C 2092 2.04 REMARK 500 N SER B 147 O HOH B 2115 2.05 REMARK 500 OE1 GLU B 92 O HOH B 2076 2.09 REMARK 500 O HOH B 2020 O HOH B 2021 2.14 REMARK 500 NH1 ARG B 3 O HOH B 2006 2.15 REMARK 500 O PRO C 71 O HOH C 2020 2.15 REMARK 500 OE2 GLU C 151 O HOH B 2121 2.19 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 O HOH B 2051 O HOH C 2024 1655 2.11 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 ILE A 115 -22.59 42.58 REMARK 500 ILE B 115 -18.07 40.87 REMARK 500 ILE C 115 -24.56 43.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2017 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH B2018 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH C2094 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH C2096 DISTANCE = 6.91 ANGSTROMS REMARK 525 HOH C2097 DISTANCE = 9.50 ANGSTROMS REMARK 525 HOH C2098 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH C2099 DISTANCE = 8.99 ANGSTROMS 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 A1153 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 YYY A1152 O1A REMARK 620 2 YYY A1152 O2B 64.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1153 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 YYY B1152 O2A REMARK 620 2 YYY B1152 O3B 72.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C1153 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 YYY C1152 O2A REMARK 620 2 HOH C2059 O 86.5 REMARK 620 3 HOH C2060 O 104.2 95.2 REMARK 620 4 HOH C2093 O 80.9 167.4 88.8 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 YYY B 1152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YYY A 1152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YYY C 1152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1153 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1153 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 1153 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UOF RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM REMARK 900 LITOPENAEUS VANNAMEI COMPLEXED WITH DADP REMARK 900 RELATED ID: 4UOH RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM REMARK 900 LITOPENAEUS VANNAMEI COMPLEXED WITH ADP DBREF 4UOG A 1 151 UNP A5J299 A5J299_LITVA 1 151 DBREF 4UOG B 1 151 UNP A5J299 A5J299_LITVA 1 151 DBREF 4UOG C 1 151 UNP A5J299 A5J299_LITVA 1 151 SEQRES 1 A 151 MET VAL ARG GLU ARG THR PHE ILE ALA VAL LYS PRO ASP SEQRES 2 A 151 GLY VAL GLN ARG GLY LEU ILE GLY GLU ILE ILE LYS ARG SEQRES 3 A 151 PHE GLU ALA LYS GLY PHE LYS LEU ALA GLY MET LYS TYR SEQRES 4 A 151 ILE GLN ALA SER GLU ASP LEU LEU LYS GLN HIS TYR ILE SEQRES 5 A 151 ASP LEU ALA ASP LYS PRO PHE TYR PRO GLY LEU CYS LYS SEQRES 6 A 151 TYR MET SER SER GLY PRO VAL VAL ALA MET CYS TRP GLU SEQRES 7 A 151 GLY THR GLY VAL VAL LYS THR ALA ARG VAL MET MET GLY SEQRES 8 A 151 GLU THR ARG PRO ALA ASP SER LYS PRO GLY THR ILE ARG SEQRES 9 A 151 GLY ASP PHE CYS ILE GLU VAL GLY ARG ASN ILE ILE HIS SEQRES 10 A 151 GLY SER ASP SER VAL GLU SER ALA ASN LYS GLU ILE ALA SEQRES 11 A 151 LEU TRP PHE LYS PRO GLU GLU LEU VAL SER TRP THR GLN SEQRES 12 A 151 THR ASN GLU SER TRP ILE TYR GLU SEQRES 1 B 151 MET VAL ARG GLU ARG THR PHE ILE ALA VAL LYS PRO ASP SEQRES 2 B 151 GLY VAL GLN ARG GLY LEU ILE GLY GLU ILE ILE LYS ARG SEQRES 3 B 151 PHE GLU ALA LYS GLY PHE LYS LEU ALA GLY MET LYS TYR SEQRES 4 B 151 ILE GLN ALA SER GLU ASP LEU LEU LYS GLN HIS TYR ILE SEQRES 5 B 151 ASP LEU ALA ASP LYS PRO PHE TYR PRO GLY LEU CYS LYS SEQRES 6 B 151 TYR MET SER SER GLY PRO VAL VAL ALA MET CYS TRP GLU SEQRES 7 B 151 GLY THR GLY VAL VAL LYS THR ALA ARG VAL MET MET GLY SEQRES 8 B 151 GLU THR ARG PRO ALA ASP SER LYS PRO GLY THR ILE ARG SEQRES 9 B 151 GLY ASP PHE CYS ILE GLU VAL GLY ARG ASN ILE ILE HIS SEQRES 10 B 151 GLY SER ASP SER VAL GLU SER ALA ASN LYS GLU ILE ALA SEQRES 11 B 151 LEU TRP PHE LYS PRO GLU GLU LEU VAL SER TRP THR GLN SEQRES 12 B 151 THR ASN GLU SER TRP ILE TYR GLU SEQRES 1 C 151 MET VAL ARG GLU ARG THR PHE ILE ALA VAL LYS PRO ASP SEQRES 2 C 151 GLY VAL GLN ARG GLY LEU ILE GLY GLU ILE ILE LYS ARG SEQRES 3 C 151 PHE GLU ALA LYS GLY PHE LYS LEU ALA GLY MET LYS TYR SEQRES 4 C 151 ILE GLN ALA SER GLU ASP LEU LEU LYS GLN HIS TYR ILE SEQRES 5 C 151 ASP LEU ALA ASP LYS PRO PHE TYR PRO GLY LEU CYS LYS SEQRES 6 C 151 TYR MET SER SER GLY PRO VAL VAL ALA MET CYS TRP GLU SEQRES 7 C 151 GLY THR GLY VAL VAL LYS THR ALA ARG VAL MET MET GLY SEQRES 8 C 151 GLU THR ARG PRO ALA ASP SER LYS PRO GLY THR ILE ARG SEQRES 9 C 151 GLY ASP PHE CYS ILE GLU VAL GLY ARG ASN ILE ILE HIS SEQRES 10 C 151 GLY SER ASP SER VAL GLU SER ALA ASN LYS GLU ILE ALA SEQRES 11 C 151 LEU TRP PHE LYS PRO GLU GLU LEU VAL SER TRP THR GLN SEQRES 12 C 151 THR ASN GLU SER TRP ILE TYR GLU HET YYY A1152 24 HET MG A1153 1 HET YYY B1152 24 HET MG B1153 1 HET YYY C1152 24 HET MG C1153 1 HETNAM YYY DEOXYCYTIDINE DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 4 YYY 3(C9 H15 N3 O10 P2) FORMUL 5 MG 3(MG 2+) FORMUL 10 HOH *319(H2 O) HELIX 1 1 LYS A 11 ARG A 17 1 7 HELIX 2 2 LEU A 19 GLY A 31 1 13 HELIX 3 3 SER A 43 TYR A 51 1 9 HELIX 4 4 ILE A 52 ALA A 55 5 4 HELIX 5 5 PHE A 59 MET A 67 1 9 HELIX 6 6 GLY A 81 GLY A 91 1 11 HELIX 7 7 ARG A 94 SER A 98 5 5 HELIX 8 8 THR A 102 CYS A 108 1 7 HELIX 9 9 SER A 121 PHE A 133 1 13 HELIX 10 10 LYS A 134 LEU A 138 5 5 HELIX 11 11 ASN A 145 TYR A 150 1 6 HELIX 12 12 LYS B 11 ARG B 17 1 7 HELIX 13 13 LEU B 19 GLY B 31 1 13 HELIX 14 14 SER B 43 TYR B 51 1 9 HELIX 15 15 ILE B 52 ALA B 55 5 4 HELIX 16 16 PHE B 59 MET B 67 1 9 HELIX 17 17 GLY B 81 GLY B 91 1 11 HELIX 18 18 ARG B 94 SER B 98 5 5 HELIX 19 19 THR B 102 CYS B 108 1 7 HELIX 20 20 GLU B 110 ASN B 114 5 5 HELIX 21 21 SER B 121 PHE B 133 1 13 HELIX 22 22 LYS B 134 LEU B 138 5 5 HELIX 23 23 ASN B 145 TYR B 150 1 6 HELIX 24 24 LYS C 11 ARG C 17 1 7 HELIX 25 25 LEU C 19 GLY C 31 1 13 HELIX 26 26 SER C 43 TYR C 51 1 9 HELIX 27 27 ILE C 52 ALA C 55 5 4 HELIX 28 28 PHE C 59 MET C 67 1 9 HELIX 29 29 GLY C 81 GLY C 91 1 11 HELIX 30 30 ARG C 94 SER C 98 5 5 HELIX 31 31 THR C 102 CYS C 108 1 7 HELIX 32 32 SER C 121 PHE C 133 1 13 HELIX 33 33 LYS C 134 LEU C 138 5 5 HELIX 34 34 ASN C 145 TYR C 150 1 6 SHEET 1 AA 4 LYS A 33 ILE A 40 0 SHEET 2 AA 4 VAL A 72 GLU A 78 -1 O VAL A 72 N ILE A 40 SHEET 3 AA 4 ARG A 5 VAL A 10 -1 O THR A 6 N TRP A 77 SHEET 4 AA 4 ILE A 116 GLY A 118 -1 O HIS A 117 N ALA A 9 SHEET 1 BA 4 LYS B 33 ILE B 40 0 SHEET 2 BA 4 VAL B 72 GLU B 78 -1 O VAL B 72 N ILE B 40 SHEET 3 BA 4 ARG B 5 VAL B 10 -1 O THR B 6 N TRP B 77 SHEET 4 BA 4 ILE B 116 GLY B 118 -1 O HIS B 117 N ALA B 9 SHEET 1 CA 4 LYS C 33 ILE C 40 0 SHEET 2 CA 4 VAL C 72 GLU C 78 -1 O VAL C 72 N ILE C 40 SHEET 3 CA 4 ARG C 5 VAL C 10 -1 O THR C 6 N TRP C 77 SHEET 4 CA 4 ILE C 116 GLY C 118 -1 O HIS C 117 N ALA C 9 LINK O1A YYY A1152 MG MG A1153 1555 1555 2.37 LINK O2B YYY A1152 MG MG A1153 1555 1555 2.90 LINK O2A YYY B1152 MG MG B1153 1555 1555 2.46 LINK O3B YYY B1152 MG MG B1153 1555 1555 2.48 LINK O2A YYY C1152 MG MG C1153 1555 1555 2.15 LINK MG MG C1153 O HOH C2059 1555 1555 2.68 LINK MG MG C1153 O HOH C2060 1555 1555 2.04 LINK MG MG C1153 O HOH C2093 1555 1555 2.47 SITE 1 AC1 15 LYS B 11 LEU B 54 PHE B 59 LEU B 63 SITE 2 AC1 15 ARG B 87 THR B 93 VAL B 111 GLY B 112 SITE 3 AC1 15 ASN B 114 MG B1153 HOH B2072 HOH B2080 SITE 4 AC1 15 HOH B2121 HOH B2123 HOH B2124 SITE 1 AC2 14 LYS A 11 TYR A 51 LEU A 54 PHE A 59 SITE 2 AC2 14 LEU A 63 ARG A 87 THR A 93 ARG A 94 SITE 3 AC2 14 ARG A 104 VAL A 111 ASN A 114 MG A1153 SITE 4 AC2 14 HOH A2013 HOH A2096 SITE 1 AC3 15 LYS C 11 TYR C 51 LEU C 54 PHE C 59 SITE 2 AC3 15 LEU C 63 ARG C 87 THR C 93 ARG C 104 SITE 3 AC3 15 VAL C 111 ASN C 114 MG C1153 HOH C2067 SITE 4 AC3 15 HOH C2071 HOH C2092 HOH C2093 SITE 1 AC4 1 YYY B1152 SITE 1 AC5 2 ASP A 120 YYY A1152 SITE 1 AC6 5 ASP C 120 YYY C1152 HOH C2059 HOH C2060 SITE 2 AC6 5 HOH C2093 CRYST1 70.160 135.370 104.820 90.00 90.00 90.00 C 2 2 21 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 0.014253 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009540 0.00000