HEADER TRANSFERASE 03-JUN-14 4UOH TITLE CRYSTALLOGRAPHIC STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE TITLE 2 FROM LITOPENAEUS VANNAMEI COMPLEXED WITH ADP 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, ADP, PURINE, WHITE-SHRIMP, BINDING KEYWDS 2 SITE, NUCLEOTIDE EXPDTA X-RAY DIFFRACTION AUTHOR A.A.LOPEZ-ZAVALA,E.GUEVARA-HERNANDEZ,V.STOJANOFF,E.RUDINO-PINERA, AUTHOR 2 R.R.SOTELO-MUNDO REVDAT 2 17-SEP-14 4UOH 1 JRNL REVDAT 1 10-SEP-14 4UOH 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 ISSN 1744-3091 JRNL PMID 25195883 JRNL DOI 10.1107/S2053230X1401557X REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.007 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.887 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.34 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.58 REMARK 3 NUMBER OF REFLECTIONS : 29447 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1800 REMARK 3 R VALUE (WORKING SET) : 0.1780 REMARK 3 FREE R VALUE : 0.2170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1497 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 34.8925 - 4.4610 1.00 2670 156 0.1712 0.1951 REMARK 3 2 4.4610 - 3.5420 1.00 2569 152 0.1537 0.1704 REMARK 3 3 3.5420 - 3.0945 1.00 2602 119 0.1614 0.2201 REMARK 3 4 3.0945 - 2.8117 1.00 2525 153 0.1767 0.2335 REMARK 3 5 2.8117 - 2.6103 1.00 2533 143 0.1903 0.2431 REMARK 3 6 2.6103 - 2.4564 1.00 2543 124 0.1904 0.2478 REMARK 3 7 2.4564 - 2.3334 1.00 2513 134 0.1906 0.2415 REMARK 3 8 2.3334 - 2.2319 1.00 2538 130 0.1993 0.2522 REMARK 3 9 2.2319 - 2.1460 1.00 2524 127 0.1941 0.2225 REMARK 3 10 2.1460 - 2.0719 1.00 2510 131 0.2079 0.2755 REMARK 3 11 2.0719 - 2.0072 0.96 2423 128 0.2411 0.2987 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 : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.18 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.19 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 : 0.007 3493 REMARK 3 ANGLE : 1.169 4720 REMARK 3 CHIRALITY : 0.081 503 REMARK 3 PLANARITY : 0.004 594 REMARK 3 DIHEDRAL : 14.657 1302 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: NO ELECTRON DENSITY WAS FOUND FOR ADP REMARK 3 IN THE CHAIN A ACTIVE SITE. ALSO NUCLEOTIDE BINDING LOOP IN CHAIN REMARK 3 A THAT COMPRISE RESIDUES 44-66 WERE DISORDERED. THEREFORE, BOTH REMARK 3 LIGAND AND DISORDERED LOOP WERE NOT INCLUDED IN IN FINAL THE REMARK 3 MODEL. REMARK 4 REMARK 4 4UOH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUN-14. REMARK 100 THE PDBE ID CODE IS EBI-60866. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-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 (QUANTUM 270) REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29462 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.00 REMARK 200 RESOLUTION RANGE LOW (A) : 34.80 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.2 REMARK 200 R MERGE (I) : 0.14 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.70 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 8.1 REMARK 200 R MERGE FOR SHELL (I) : 0.74 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.40 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: SHRIMP NDK STRUCTURE TO BE DEPOSITED REMARK 200 REMARK 200 REMARK: THE STARTING MODEL WAS PREVIOUS LITOPENAEUS REMARK 200 VANNAMEI NDK STRUCTURE COMPLEXED WITH DADP WHICH WILL BE REMARK 200 DEPOSITED IN PDB REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.5 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.1 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE REMARK 280 HEXAHYDRATE, 0.1 M TRIS-HCL PH 8.5 AND 30% (W/V) PEG 4,000 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 51.63650 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 51.63650 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 34.90300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.41750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.90300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.41750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.63650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.90300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 60.41750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.63650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.90300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 60.41750 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: 19550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -136.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, 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 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 51.63650 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2138 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2140 LIES ON A SPECIAL POSITION. 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 GLU A 44 REMARK 465 ASP A 45 REMARK 465 LEU A 46 REMARK 465 LEU A 47 REMARK 465 LYS A 48 REMARK 465 GLN A 49 REMARK 465 HIS A 50 REMARK 465 TYR A 51 REMARK 465 ILE A 52 REMARK 465 ASP A 53 REMARK 465 LEU A 54 REMARK 465 ALA A 55 REMARK 465 ASP A 56 REMARK 465 LYS A 57 REMARK 465 PRO A 58 REMARK 465 PHE A 59 REMARK 465 TYR A 60 REMARK 465 PRO A 61 REMARK 465 GLY A 62 REMARK 465 LEU A 63 REMARK 465 CYS A 64 REMARK 465 LYS A 65 REMARK 465 TYR A 66 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 A 1 CG SD CE REMARK 470 MET A 67 CB CG SD CE REMARK 470 MET B 1 CG SD CE 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 NZ LYS A 84 O HOH A 2077 2.19 REMARK 500 OE1 GLU A 146 O HOH A 2053 2.11 REMARK 500 OD2 ASP B 97 O HOH B 2104 2.10 REMARK 500 O3B ADP C 1152 O HOH C 2126 2.11 REMARK 500 O2A ADP C 1152 O HOH C 2126 2.03 REMARK 500 O HOH A 2013 O HOH A 2050 2.01 REMARK 500 O HOH A 2070 O HOH A 2124 1.99 REMARK 500 O HOH A 2084 O HOH A 2113 2.15 REMARK 500 O HOH A 2099 O HOH A 2102 2.16 REMARK 500 O HOH A 2137 O HOH A 2141 2.04 REMARK 500 O HOH A 2141 O HOH A 2142 2.16 REMARK 500 O HOH B 2008 O HOH B 2017 2.09 REMARK 500 O HOH B 2046 O HOH A 2062 2.16 REMARK 500 O HOH B 2124 O HOH B 2125 1.63 REMARK 500 O HOH C 2026 O HOH C 2028 2.18 REMARK 500 O HOH C 2030 O HOH C 2066 1.95 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 A 2036 O HOH A 2038 3555 2.12 REMARK 500 O HOH B 2003 O HOH C 2071 1655 2.10 REMARK 500 O HOH B 2037 O HOH C 2042 3555 2.16 REMARK 500 O HOH C 2066 O HOH B 2107 8445 2.15 REMARK 500 O HOH C 2124 O HOH C 2124 3555 1.99 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 ARG C 3 C - N - CA ANGL. DEV. = 22.7 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 ILE A 115 -28.02 51.61 REMARK 500 ILE B 115 -18.00 44.87 REMARK 500 ILE C 115 -24.32 50.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ILE A 115 23.9 L L OUTSIDE RANGE REMARK 500 ILE B 115 24.2 L L OUTSIDE RANGE REMARK 500 ILE C 115 22.6 L L OUTSIDE RANGE 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 B1153 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP B1152 O2A REMARK 620 2 HOH B2124 O 70.4 REMARK 620 3 HOH B2125 O 70.2 44.0 REMARK 620 4 ADP B1152 O3B 72.9 123.7 84.0 REMARK 620 5 HOH B2122 O 171.2 116.0 109.6 98.3 REMARK 620 N 1 2 3 4 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 ADP C1152 O2A REMARK 620 2 HOH C2060 O 107.5 REMARK 620 3 HOH C2063 O 109.7 94.8 REMARK 620 4 HOH C2107 O 86.8 164.1 86.5 REMARK 620 5 HOH C2126 O 63.0 104.3 160.8 75.6 REMARK 620 6 HOH C2108 O 161.4 78.4 86.9 85.9 98.7 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 ADP C1152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B1152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1153 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C1153 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UOF RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE REMARK 900 FROM LITOPENAEUS VANNAMEI COMPLEXED WITH DADP REMARK 900 RELATED ID: 4UOG RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE REMARK 900 FROM LITOPENAEUS VANNAMEI COMPLEXED WITH DCDP DBREF 4UOH A 1 151 UNP A5J299 A5J299_LITVA 1 151 DBREF 4UOH B 1 151 UNP A5J299 A5J299_LITVA 1 151 DBREF 4UOH 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 ADP C1152 27 HET ADP B1152 27 HET MG B1153 1 HET MG C1153 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 4 ADP 2(C10 H15 N5 O10 P2) FORMUL 5 MG 2(MG 2+) FORMUL 6 HOH *419(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 GLY A 81 GLY A 91 1 11 HELIX 4 4 ARG A 94 SER A 98 5 5 HELIX 5 5 THR A 102 CYS A 108 1 7 HELIX 6 6 GLU A 110 ASN A 114 5 5 HELIX 7 7 SER A 121 PHE A 133 1 13 HELIX 8 8 LYS A 134 LEU A 138 5 5 HELIX 9 9 GLN A 143 ILE A 149 5 7 HELIX 10 10 LYS B 11 ARG B 17 1 7 HELIX 11 11 LEU B 19 GLY B 31 1 13 HELIX 12 12 SER B 43 TYR B 51 1 9 HELIX 13 13 ILE B 52 ALA B 55 5 4 HELIX 14 14 PHE B 59 SER B 68 1 10 HELIX 15 15 GLY B 81 GLY B 91 1 11 HELIX 16 16 ARG B 94 SER B 98 5 5 HELIX 17 17 THR B 102 CYS B 108 1 7 HELIX 18 18 SER B 121 PHE B 133 1 13 HELIX 19 19 LYS B 134 LEU B 138 5 5 HELIX 20 20 GLN B 143 ILE B 149 5 7 HELIX 21 21 LYS C 11 ARG C 17 1 7 HELIX 22 22 LEU C 19 GLY C 31 1 13 HELIX 23 23 SER C 43 TYR C 51 1 9 HELIX 24 24 ILE C 52 ALA C 55 5 4 HELIX 25 25 PHE C 59 SER C 68 1 10 HELIX 26 26 GLY C 81 GLY C 91 1 11 HELIX 27 27 ARG C 94 SER C 98 5 5 HELIX 28 28 THR C 102 CYS C 108 1 7 HELIX 29 29 GLU C 110 ASN C 114 5 5 HELIX 30 30 SER C 121 PHE C 133 1 13 HELIX 31 31 LYS C 134 LEU C 138 5 5 HELIX 32 32 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 O3B ADP B1152 MG MG B1153 1555 1555 2.44 LINK O2A ADP B1152 MG MG B1153 1555 1555 2.05 LINK MG MG B1153 O HOH B2124 1555 1555 2.07 LINK MG MG B1153 O HOH B2125 1555 1555 2.26 LINK MG MG B1153 O HOH B2122 1555 1555 2.05 LINK O2A ADP C1152 MG MG C1153 1555 1555 1.98 LINK MG MG C1153 O HOH C2063 1555 1555 1.98 LINK MG MG C1153 O HOH C2107 1555 1555 2.02 LINK MG MG C1153 O HOH C2126 1555 1555 1.90 LINK MG MG C1153 O HOH C2108 1555 1555 2.27 LINK MG MG C1153 O HOH C2060 1555 1555 2.07 SITE 1 AC1 19 LYS C 11 TYR C 51 LEU C 54 PHE C 59 SITE 2 AC1 19 LEU C 63 ARG C 87 THR C 93 ARG C 94 SITE 3 AC1 19 VAL C 111 ASN C 114 MG C1153 HOH C2017 SITE 4 AC1 19 HOH C2082 HOH C2083 HOH C2091 HOH C2107 SITE 5 AC1 19 HOH C2126 HOH C2127 HOH C2128 SITE 1 AC2 17 LYS B 11 TYR B 51 LEU B 54 PHE B 59 SITE 2 AC2 17 LEU B 63 ARG B 87 THR B 93 ARG B 94 SITE 3 AC2 17 VAL B 111 ASN B 114 MG B1153 HOH B2025 SITE 4 AC2 17 HOH B2090 HOH B2096 HOH B2124 HOH B2125 SITE 5 AC2 17 HOH B2144 SITE 1 AC3 4 ADP B1152 HOH B2122 HOH B2124 HOH B2125 SITE 1 AC4 7 ASP C 120 ADP C1152 HOH C2060 HOH C2063 SITE 2 AC4 7 HOH C2107 HOH C2108 HOH C2126 CRYST1 69.806 120.835 103.273 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 0.014325 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008276 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009683 0.00000