HEADER TRANSFERASE 13-JUN-10 3NGU TITLE STRUCTURE OF LEISHMANIA NDKB COMPLEXED WITH ADP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.4.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 ORGANISM_TAXID: 5664; SOURCE 4 GENE: L1648.07, LMJF32.2950, NDKB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS NDKB, ADP, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.M.TRINDADE,T.A.C.B.SOUSA,C.C.C.TONOLI,C.R.SANTOS,R.K.ARNI,R.J.WARD, AUTHOR 2 A.H.C.OLIVEIRA,M.T.MURAKAMI REVDAT 6 21-FEB-24 3NGU 1 REMARK REVDAT 5 08-NOV-17 3NGU 1 REMARK REVDAT 4 09-OCT-13 3NGU 1 AUTHOR VERSN REVDAT 3 29-JUN-11 3NGU 1 JRNL REVDAT 2 18-MAY-11 3NGU 1 JRNL REVDAT 1 27-APR-11 3NGU 0 JRNL AUTH T.A.SOUZA,D.M.TRINDADE,C.C.TONOLI,C.R.SANTOS,R.J.WARD, JRNL AUTH 2 R.K.ARNI,A.H.OLIVEIRA,M.T.MURAKAMI JRNL TITL MOLECULAR ADAPTABILITY OF NUCLEOSIDE DIPHOSPHATE KINASE B JRNL TITL 2 FROM TRYPANOSOMATID PARASITES: STABILITY, OLIGOMERIZATION JRNL TITL 3 AND STRUCTURAL DETERMINANTS OF NUCLEOTIDE BINDING. JRNL REF MOL BIOSYST V. 7 2189 2011 JRNL REFN ISSN 1742-206X JRNL PMID 21528129 JRNL DOI 10.1039/C0MB00307G REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 16313 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 886 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1087 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.4240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2346 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 39 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.30000 REMARK 3 B22 (A**2) : -4.30000 REMARK 3 B33 (A**2) : 6.44000 REMARK 3 B12 (A**2) : -2.15000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.309 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.259 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.183 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.316 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2426 ; 0.040 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3301 ; 2.934 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 302 ; 8.004 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;32.278 ;23.131 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 380 ;19.474 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;23.703 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 360 ; 0.217 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1830 ; 0.017 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1500 ; 1.801 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2411 ; 2.933 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 926 ; 4.924 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 889 ; 6.751 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.00 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3NGU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059811. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.458 REMARK 200 MONOCHROMATOR : SILICON DOUBLE-CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17366 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 32.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 8.30 REMARK 200 R MERGE FOR SHELL (I) : 0.43600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350 SODIUM SULPHATE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 61.60650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.56853 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 45.99433 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 61.60650 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 35.56853 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 45.99433 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 61.60650 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 35.56853 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 45.99433 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 61.60650 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 35.56853 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 45.99433 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 61.60650 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 35.56853 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 45.99433 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 61.60650 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 35.56853 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 45.99433 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 71.13706 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 91.98867 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 71.13706 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 91.98867 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 71.13706 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 91.98867 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 71.13706 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 91.98867 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 71.13706 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 91.98867 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 71.13706 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 91.98867 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 19530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 52 CB CG CD CE NZ REMARK 480 ASP A 53 CG OD1 OD2 REMARK 480 LYS A 80 CD CE NZ REMARK 480 LYS A 84 CE NZ REMARK 480 LYS A 134 CD CE NZ REMARK 480 ASP A 136 CG OD1 OD2 REMARK 480 LYS B 52 CE NZ REMARK 480 ASP B 53 CG OD1 OD2 REMARK 480 GLU B 123 CG CD OE1 OE2 REMARK 480 GLU B 126 CG CD OE1 OE2 REMARK 480 LYS B 134 CG CD CE NZ 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 GLU A 4 CG GLU A 4 CD 0.124 REMARK 500 LYS A 11 CE LYS A 11 NZ 0.162 REMARK 500 PHE A 27 CZ PHE A 27 CE2 0.140 REMARK 500 LYS A 33 CD LYS A 33 CE 0.152 REMARK 500 GLN A 46 CG GLN A 46 CD 0.143 REMARK 500 LYS A 52 CA LYS A 52 CB -0.169 REMARK 500 ASP A 53 CB ASP A 53 CG -0.206 REMARK 500 TYR A 66 CD1 TYR A 66 CE1 0.106 REMARK 500 LYS A 80 CG LYS A 80 CD -0.214 REMARK 500 SER A 98 CB SER A 98 OG -0.101 REMARK 500 VAL A 115 CB VAL A 115 CG2 -0.132 REMARK 500 GLU A 123 CG GLU A 123 CD 0.101 REMARK 500 GLU A 126 CG GLU A 126 CD 0.119 REMARK 500 GLU A 126 CD GLU A 126 OE1 0.067 REMARK 500 PHE A 133 CZ PHE A 133 CE2 0.142 REMARK 500 LYS A 134 CG LYS A 134 CD -0.325 REMARK 500 ASP A 136 CB ASP A 136 CG -0.238 REMARK 500 GLU B 22 CG GLU B 22 CD 0.117 REMARK 500 ILE B 23 CA ILE B 23 CB 0.158 REMARK 500 PHE B 27 CZ PHE B 27 CE2 0.142 REMARK 500 GLU B 28 CG GLU B 28 CD 0.114 REMARK 500 GLU B 28 CD GLU B 28 OE2 0.069 REMARK 500 VAL B 35 CA VAL B 35 CB 0.167 REMARK 500 LYS B 52 CD LYS B 52 CE -0.308 REMARK 500 ASP B 53 CB ASP B 53 CG 0.205 REMARK 500 VAL B 73 CB VAL B 73 CG2 -0.137 REMARK 500 CYS B 74 CB CYS B 74 SG -0.143 REMARK 500 LYS B 80 CB LYS B 80 CG 0.176 REMARK 500 VAL B 115 CB VAL B 115 CG2 -0.135 REMARK 500 GLU B 123 CB GLU B 123 CG 0.168 REMARK 500 ALA B 125 CA ALA B 125 CB 0.173 REMARK 500 TRP B 141 CB TRP B 141 CG 0.127 REMARK 500 TYR B 150 CD1 TYR B 150 CE1 0.128 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 A 5 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 LEU A 37 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 ASP A 136 CA - CB - CG ANGL. DEV. = 16.8 DEGREES REMARK 500 ASP A 136 CB - CG - OD1 ANGL. DEV. = -17.8 DEGREES REMARK 500 ASP A 136 CB - CG - OD2 ANGL. DEV. = 14.8 DEGREES REMARK 500 GLU A 151 CA - C - O ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG B 5 NH1 - CZ - NH2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG B 5 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG B 26 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP B 53 CA - CB - CG ANGL. DEV. = -25.1 DEGREES REMARK 500 ASP B 53 CB - CG - OD1 ANGL. DEV. = -16.0 DEGREES REMARK 500 ASP B 53 CB - CG - OD2 ANGL. DEV. = 15.9 DEGREES REMARK 500 LEU B 54 CA - CB - CG ANGL. DEV. = 18.2 DEGREES REMARK 500 GLU B 123 CA - CB - CG ANGL. DEV. = -22.4 DEGREES REMARK 500 LYS B 134 CA - CB - CG ANGL. DEV. = 13.4 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 52 -53.94 -19.58 REMARK 500 VAL A 115 -33.40 72.00 REMARK 500 ASP A 136 -33.58 94.62 REMARK 500 HIS A 144 0.71 -65.26 REMARK 500 VAL B 35 -4.45 -143.40 REMARK 500 ALA B 36 140.18 -172.81 REMARK 500 ASP B 53 8.11 -62.70 REMARK 500 VAL B 115 -30.89 73.37 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 TYR A 150 GLU A 151 145.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 152 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NGR RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH UNORDERED NUCLEOTIDE-BINDING LOOP. REMARK 900 RELATED ID: 3NGS RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH ORDERED NUCLEOTIDE-BINDING LOOP. REMARK 900 RELATED ID: 3NGT RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AMP. DBREF 3NGU A 1 151 UNP Q9U1E1 Q9U1E1_LEIMA 1 151 DBREF 3NGU B 1 151 UNP Q9U1E1 Q9U1E1_LEIMA 1 151 SEQRES 1 A 151 MET SER SER GLU ARG THR PHE ILE ALA VAL LYS PRO ASP SEQRES 2 A 151 GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE ALA ARG SEQRES 3 A 151 PHE GLU ARG LYS GLY TYR LYS LEU VAL ALA LEU LYS ILE SEQRES 4 A 151 LEU GLN PRO THR THR GLU GLN ALA GLN GLY HIS TYR LYS SEQRES 5 A 151 ASP LEU CYS SER LYS PRO PHE PHE PRO ALA LEU VAL LYS SEQRES 6 A 151 TYR PHE SER SER GLY PRO ILE VAL CYS MET VAL TRP GLU SEQRES 7 A 151 GLY LYS ASN VAL VAL LYS SER GLY ARG VAL LEU LEU GLY SEQRES 8 A 151 ALA THR ASN PRO ALA ASP SER GLN PRO GLY THR ILE ARG SEQRES 9 A 151 GLY ASP PHE ALA VAL ASP VAL GLY ARG ASN VAL CYS HIS SEQRES 10 A 151 GLY SER ASP SER VAL GLU SER ALA GLU ARG GLU ILE ALA SEQRES 11 A 151 PHE TRP PHE LYS ALA ASP GLU ILE ALA SER TRP THR SER SEQRES 12 A 151 HIS SER VAL SER GLN ILE TYR GLU SEQRES 1 B 151 MET SER SER GLU ARG THR PHE ILE ALA VAL LYS PRO ASP SEQRES 2 B 151 GLY VAL GLN ARG GLY LEU VAL GLY GLU ILE ILE ALA ARG SEQRES 3 B 151 PHE GLU ARG LYS GLY TYR LYS LEU VAL ALA LEU LYS ILE SEQRES 4 B 151 LEU GLN PRO THR THR GLU GLN ALA GLN GLY HIS TYR LYS SEQRES 5 B 151 ASP LEU CYS SER LYS PRO PHE PHE PRO ALA LEU VAL LYS SEQRES 6 B 151 TYR PHE SER SER GLY PRO ILE VAL CYS MET VAL TRP GLU SEQRES 7 B 151 GLY LYS ASN VAL VAL LYS SER GLY ARG VAL LEU LEU GLY SEQRES 8 B 151 ALA THR ASN PRO ALA ASP SER GLN PRO GLY THR ILE ARG SEQRES 9 B 151 GLY ASP PHE ALA VAL ASP VAL GLY ARG ASN VAL CYS HIS SEQRES 10 B 151 GLY SER ASP SER VAL GLU SER ALA GLU ARG GLU ILE ALA SEQRES 11 B 151 PHE TRP PHE LYS ALA ASP GLU ILE ALA SER TRP THR SER SEQRES 12 B 151 HIS SER VAL SER GLN ILE TYR GLU HET ADP A 152 27 HET ADP B 152 27 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 5 HOH *39(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 THR A 43 TYR A 51 1 9 HELIX 4 4 LYS A 52 CYS A 55 5 4 HELIX 5 5 PHE A 59 SER A 68 1 10 HELIX 6 6 ASN A 81 GLY A 91 1 11 HELIX 7 7 ASN A 94 SER A 98 5 5 HELIX 8 8 THR A 102 ALA A 108 1 7 HELIX 9 9 SER A 121 PHE A 133 1 13 HELIX 10 10 SER A 145 TYR A 150 1 6 HELIX 11 11 LYS B 11 ARG B 17 1 7 HELIX 12 12 LEU B 19 LYS B 30 1 12 HELIX 13 13 THR B 43 TYR B 51 1 9 HELIX 14 14 LYS B 52 CYS B 55 5 4 HELIX 15 15 PHE B 59 SER B 68 1 10 HELIX 16 16 ASN B 81 GLY B 91 1 11 HELIX 17 17 ASN B 94 SER B 98 5 5 HELIX 18 18 THR B 102 ALA B 108 1 7 HELIX 19 19 ASP B 110 ASN B 114 5 5 HELIX 20 20 SER B 121 PHE B 133 1 13 HELIX 21 21 LYS B 134 ILE B 138 5 5 HELIX 22 22 SER B 145 TYR B 150 1 6 SHEET 1 A 4 LYS A 33 LEU A 40 0 SHEET 2 A 4 ILE A 72 GLU A 78 -1 O GLU A 78 N LYS A 33 SHEET 3 A 4 ARG A 5 VAL A 10 -1 N VAL A 10 O VAL A 73 SHEET 4 A 4 CYS A 116 GLY A 118 -1 O HIS A 117 N ALA A 9 SHEET 1 B 4 LYS B 33 LEU B 40 0 SHEET 2 B 4 ILE B 72 GLU B 78 -1 O GLU B 78 N LYS B 33 SHEET 3 B 4 ARG B 5 VAL B 10 -1 N ILE B 8 O MET B 75 SHEET 4 B 4 CYS B 116 GLY B 118 -1 O HIS B 117 N ALA B 9 SITE 1 AC1 8 LYS A 11 PHE A 59 LEU A 63 ARG A 87 SITE 2 AC1 8 THR A 93 ARG A 104 VAL A 111 ASN A 114 SITE 1 AC2 7 LYS B 11 PHE B 59 LEU B 63 ARG B 87 SITE 2 AC2 7 THR B 93 VAL B 111 ASN B 114 CRYST1 123.213 123.213 137.983 90.00 90.00 120.00 H 3 2 36 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 0.008116 0.004686 0.000000 0.00000 SCALE2 0.000000 0.009372 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007247 0.00000