HEADER TRANSFERASE 06-JAN-11 3Q86 TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS NUCLEOSIDE DIPHOSPHATE TITLE 2 KINASE COMPLEXED WITH GTP 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: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS; SOURCE 3 ORGANISM_TAXID: 93062; SOURCE 4 STRAIN: COL; SOURCE 5 GENE: NDK, SACOL1509; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS FERRIDOXIN FOLD, ALPHA-BETA PROTEIN FAMILY, NUCLEOSIDE DIPHOSPHATE KEYWDS 2 KINASES (NDKS), TRANSFER, A GAMMA PHOSPHATE, NUCLEOSIDE KEYWDS 3 TRIPHOSPHATES, NUCLEOSIDE DIPHOSPHATE, NUCLEOTIDE BINDING MAGNESIUM, KEYWDS 4 METAL BINDING, PHOSPHORYLATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.K.SRIVASTAVA,K.RAJASREE,B.GOPAL REVDAT 3 01-NOV-23 3Q86 1 REMARK SEQADV LINK REVDAT 2 26-JUN-13 3Q86 1 JRNL REVDAT 1 27-JUL-11 3Q86 0 JRNL AUTH S.K.SRIVASTAVA,K.RAJASREE,B.GOPAL JRNL TITL CONFORMATIONAL BASIS FOR SUBSTRATE RECOGNITION AND JRNL TITL 2 REGULATION OF CATALYTIC ACTIVITY IN STAPHYLOCOCCUS AUREUS JRNL TITL 3 NUCLEOSIDE DI-PHOSPHATE KINASE. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1814 1349 2011 JRNL REFN ISSN 0006-3002 JRNL PMID 21745603 JRNL DOI 10.1016/J.BBAPAP.2011.06.008 REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12456 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 644 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) : 2.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 822 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.1750 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2290 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 135 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.239 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.553 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 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): 2428 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3302 ; 1.926 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 296 ; 6.983 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;34.888 ;23.889 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 404 ;16.842 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;25.788 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 362 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1816 ; 0.008 ; 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): 1476 ; 0.794 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2378 ; 1.555 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 952 ; 2.782 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 924 ; 4.678 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 149 2 REMARK 3 1 B 1 B 149 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 580 ; 0.07 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 549 ; 0.09 ; 0.50 REMARK 3 TIGHT THERMAL 1 B (A**2): 580 ; 0.21 ; 0.50 REMARK 3 MEDIUM THERMAL 1 B (A**2): 549 ; 0.22 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3Q86 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063315. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : CUK (ALPHA) REMARK 200 OPTICS : GOEBEL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13104 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360 REMARK 200 RESOLUTION RANGE LOW (A) : 37.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 46.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.08100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 20.40 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: 3Q83 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MGACETATE, 0.1M CITRIC ACID, PH REMARK 280 5, 14% PEG 8000 , MICROBATCH CRYSTALLIZATION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+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 1.000000 0.000000 0.000000 37.65100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.73781 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.57067 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 37.65100 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 21.73781 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.57067 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 37.65100 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 21.73781 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.57067 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.47563 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 103.14133 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 43.47563 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 103.14133 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 43.47563 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 103.14133 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 37.65100 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -65.21344 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 75.30200 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 37.65100 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -65.21344 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 75.30200 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 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 LEU A 150 REMARK 465 GLU A 151 REMARK 465 HIS A 152 REMARK 465 HIS A 153 REMARK 465 HIS A 154 REMARK 465 HIS A 155 REMARK 465 HIS A 156 REMARK 465 HIS A 157 REMARK 465 LEU B 150 REMARK 465 GLU B 151 REMARK 465 HIS B 152 REMARK 465 HIS B 153 REMARK 465 HIS B 154 REMARK 465 HIS B 155 REMARK 465 HIS B 156 REMARK 465 HIS B 157 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 43 O CG CD OE1 OE2 REMARK 470 GLU A 121 C O CG CD OE1 OE2 REMARK 470 GLU A 124 C O CG CD OE1 OE2 REMARK 470 GLU A 133 CG CD OE1 OE2 REMARK 470 GLN B 53 CB CG CD OE1 NE2 REMARK 470 GLU B 121 O CG CD OE1 OE2 REMARK 470 GLU B 124 O CG CD OE1 OE2 REMARK 470 GLU B 133 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 N GLY A 54 O HOH A 202 1.52 REMARK 500 CA GLY A 54 O HOH A 212 1.63 REMARK 500 C4' GTP B 158 O HOH B 212 1.76 REMARK 500 C5' GTP A 158 O HOH A 227 1.76 REMARK 500 C GLY A 54 O HOH A 212 1.82 REMARK 500 O GLN A 53 O HOH A 212 1.89 REMARK 500 O5' GTP B 158 O HOH B 212 2.03 REMARK 500 CB ASN A 82 O HOH A 201 2.04 REMARK 500 CB ASN B 82 O HOH B 205 2.08 REMARK 500 OE1 GLU B 95 O HOH B 192 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 A 223 O HOH B 219 9544 1.94 REMARK 500 OE2 GLU A 149 N2 GTP A 158 3655 1.95 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 GLU B 43 CG GLU B 43 CD 0.110 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 15 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 102 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 102 NE - CZ - NH2 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 15 NE - CZ - NH1 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG B 15 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 102 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG B 102 NE - CZ - NH2 ANGL. DEV. = 5.3 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 113 -48.60 74.90 REMARK 500 ILE B 113 -44.29 77.14 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 159 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP A 158 O2B REMARK 620 2 GTP A 158 O1A 92.6 REMARK 620 3 GTP A 158 O5' 56.4 59.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 159 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP B 158 O2A REMARK 620 2 GTP B 158 O2G 93.2 REMARK 620 3 GTP B 158 O1B 75.7 73.6 REMARK 620 4 HOH B 195 O 147.6 92.3 75.4 REMARK 620 5 HOH B 196 O 83.3 164.1 90.5 82.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A 158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 159 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP B 158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 159 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3Q83 RELATED DB: PDB REMARK 900 RELATED ID: 3Q89 RELATED DB: PDB REMARK 900 RELATED ID: 3Q8U RELATED DB: PDB REMARK 900 RELATED ID: 3Q8V RELATED DB: PDB REMARK 900 RELATED ID: 3Q8Y RELATED DB: PDB DBREF 3Q86 A 1 149 UNP Q5HFV4 NDK_STAAC 1 149 DBREF 3Q86 B 1 149 UNP Q5HFV4 NDK_STAAC 1 149 SEQADV 3Q86 LEU A 150 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 GLU A 151 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 HIS A 152 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 HIS A 153 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 HIS A 154 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 HIS A 155 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 HIS A 156 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 HIS A 157 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 LEU B 150 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 GLU B 151 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 HIS B 152 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 HIS B 153 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 HIS B 154 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 HIS B 155 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 HIS B 156 UNP Q5HFV4 EXPRESSION TAG SEQADV 3Q86 HIS B 157 UNP Q5HFV4 EXPRESSION TAG SEQRES 1 A 157 MET GLU ARG THR PHE LEU MET ILE LYS PRO ASP ALA VAL SEQRES 2 A 157 GLN ARG ASN LEU ILE GLY GLU VAL ILE SER ARG ILE GLU SEQRES 3 A 157 ARG LYS GLY LEU LYS LEU VAL GLY GLY LYS LEU MET GLN SEQRES 4 A 157 VAL PRO MET GLU LEU ALA GLU THR HIS TYR GLY GLU HIS SEQRES 5 A 157 GLN GLY LYS PRO PHE TYR ASN ASP LEU ILE SER PHE ILE SEQRES 6 A 157 THR SER ALA PRO VAL PHE ALA MET VAL VAL GLU GLY GLU SEQRES 7 A 157 ASP ALA VAL ASN VAL SER ARG HIS ILE ILE GLY SER THR SEQRES 8 A 157 ASN PRO SER GLU ALA SER PRO GLY SER ILE ARG GLY ASP SEQRES 9 A 157 LEU GLY LEU THR VAL GLY ARG ASN ILE ILE HIS GLY SER SEQRES 10 A 157 ASP SER LEU GLU SER ALA GLU ARG GLU ILE ASN LEU TRP SEQRES 11 A 157 PHE ASN GLU ASN GLU ILE THR SER TYR ALA SER PRO ARG SEQRES 12 A 157 ASP ALA TRP LEU TYR GLU LEU GLU HIS HIS HIS HIS HIS SEQRES 13 A 157 HIS SEQRES 1 B 157 MET GLU ARG THR PHE LEU MET ILE LYS PRO ASP ALA VAL SEQRES 2 B 157 GLN ARG ASN LEU ILE GLY GLU VAL ILE SER ARG ILE GLU SEQRES 3 B 157 ARG LYS GLY LEU LYS LEU VAL GLY GLY LYS LEU MET GLN SEQRES 4 B 157 VAL PRO MET GLU LEU ALA GLU THR HIS TYR GLY GLU HIS SEQRES 5 B 157 GLN GLY LYS PRO PHE TYR ASN ASP LEU ILE SER PHE ILE SEQRES 6 B 157 THR SER ALA PRO VAL PHE ALA MET VAL VAL GLU GLY GLU SEQRES 7 B 157 ASP ALA VAL ASN VAL SER ARG HIS ILE ILE GLY SER THR SEQRES 8 B 157 ASN PRO SER GLU ALA SER PRO GLY SER ILE ARG GLY ASP SEQRES 9 B 157 LEU GLY LEU THR VAL GLY ARG ASN ILE ILE HIS GLY SER SEQRES 10 B 157 ASP SER LEU GLU SER ALA GLU ARG GLU ILE ASN LEU TRP SEQRES 11 B 157 PHE ASN GLU ASN GLU ILE THR SER TYR ALA SER PRO ARG SEQRES 12 B 157 ASP ALA TRP LEU TYR GLU LEU GLU HIS HIS HIS HIS HIS SEQRES 13 B 157 HIS HET GTP A 158 32 HET MG A 159 1 HET GTP B 158 32 HET MG B 159 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 GTP 2(C10 H16 N5 O14 P3) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *135(H2 O) HELIX 1 1 LYS A 9 ARG A 15 1 7 HELIX 2 2 LEU A 17 LYS A 28 1 12 HELIX 3 3 PRO A 41 TYR A 49 1 9 HELIX 4 4 GLY A 50 GLN A 53 5 4 HELIX 5 5 PHE A 57 THR A 66 1 10 HELIX 6 6 ASP A 79 GLY A 89 1 11 HELIX 7 7 SER A 100 GLY A 106 1 7 HELIX 8 8 SER A 119 GLU A 121 1 3 HELIX 9 9 SER A 122 GLU A 124 1 3 HELIX 10 10 ARG A 125 PHE A 131 1 7 HELIX 11 11 ASN A 132 ILE A 136 5 5 HELIX 12 12 ARG A 143 TYR A 148 1 6 HELIX 13 13 LYS B 9 ARG B 15 1 7 HELIX 14 14 LEU B 17 ARG B 27 1 11 HELIX 15 15 PRO B 41 TYR B 49 1 9 HELIX 16 16 GLY B 50 GLN B 53 5 4 HELIX 17 17 PHE B 57 THR B 66 1 10 HELIX 18 18 ASP B 79 GLY B 89 1 11 HELIX 19 19 SER B 100 GLY B 106 1 7 HELIX 20 20 SER B 119 PHE B 131 1 13 HELIX 21 21 ASN B 132 ILE B 136 5 5 HELIX 22 22 ARG B 143 TYR B 148 1 6 SHEET 1 A 4 LYS A 31 MET A 38 0 SHEET 2 A 4 VAL A 70 GLU A 76 -1 O GLU A 76 N LYS A 31 SHEET 3 A 4 ARG A 3 ILE A 8 -1 N ILE A 8 O PHE A 71 SHEET 4 A 4 ILE A 114 GLY A 116 -1 O HIS A 115 N MET A 7 SHEET 1 B 4 LYS B 31 MET B 38 0 SHEET 2 B 4 VAL B 70 GLU B 76 -1 O GLU B 76 N LYS B 31 SHEET 3 B 4 ARG B 3 ILE B 8 -1 N ILE B 8 O PHE B 71 SHEET 4 B 4 ILE B 114 GLY B 116 -1 O HIS B 115 N MET B 7 LINK O2B GTP A 158 MG MG A 159 1555 1555 1.86 LINK O1A GTP A 158 MG MG A 159 1555 1555 2.23 LINK O5' GTP A 158 MG MG A 159 1555 1555 2.93 LINK O2A GTP B 158 MG MG B 159 1555 1555 1.84 LINK O2G GTP B 158 MG MG B 159 1555 1555 2.07 LINK O1B GTP B 158 MG MG B 159 1555 1555 2.69 LINK MG MG B 159 O HOH B 195 1555 1555 2.22 LINK MG MG B 159 O HOH B 196 1555 1555 2.29 SITE 1 AC1 15 LYS A 9 TYR A 49 HIS A 52 PHE A 57 SITE 2 AC1 15 THR A 91 VAL A 109 GLY A 110 ASN A 112 SITE 3 AC1 15 HIS A 115 GLU A 149 MG A 159 HOH A 206 SITE 4 AC1 15 HOH A 218 HOH A 227 HOH B 210 SITE 1 AC2 3 THR A 91 ARG A 102 GTP A 158 SITE 1 AC3 20 LYS B 9 TYR B 49 HIS B 52 PHE B 57 SITE 2 AC3 20 THR B 91 ARG B 102 VAL B 109 GLY B 110 SITE 3 AC3 20 ASN B 112 HIS B 115 GLY B 116 MG B 159 SITE 4 AC3 20 HOH B 179 HOH B 195 HOH B 196 HOH B 208 SITE 5 AC3 20 HOH B 209 HOH B 210 HOH B 211 HOH B 212 SITE 1 AC4 3 GTP B 158 HOH B 195 HOH B 196 CRYST1 75.302 75.302 154.712 90.00 90.00 120.00 H 3 18 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 0.013280 0.007667 0.000000 0.00000 SCALE2 0.000000 0.015334 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006464 0.00000