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- PDB-4and: CRYSTAL FORM II OF THE D93N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINA... -

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Basic information

Entry
Database: PDB / ID: 4and
TitleCRYSTAL FORM II OF THE D93N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsNUCLEOSIDE DIPHOSPHATE KINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


symbiont-mediated perturbation of host Rab small GTPase signal transduction / purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / symbiont-mediated killing of host cell / nuclease activity / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process ...symbiont-mediated perturbation of host Rab small GTPase signal transduction / purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / symbiont-mediated killing of host cell / nuclease activity / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / phosphoprotein phosphatase activity / Prevention of phagosomal-lysosomal fusion / symbiont-mediated suppression of host innate immune response / extracellular region / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate kinase / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.808 Å
AuthorsGeorgescauld, F. / Moynie, L. / Habersetzer, J. / Lascu, I. / Dautant, A.
Citation
Journal: Plos One / Year: 2013
Title: Intersubunit Ionic Interactions Stabilize the Nucleoside Diphosphate Kinase of Mycobacterium Tuberculosis.
Authors: Georgescauld, F. / Moynie, L. / Habersetzer, J. / Cervoni, L. / Mocan, I. / Borza, T. / Harris, P. / Dautant, A. / Lascu, I.
#1: Journal: Proteins / Year: 2002
Title: X-Ray Structure of Mycobacterium Tuberculosis Nucleoside Diphosphate Kinase.
Authors: Chen, Y. / Morera, S. / Mocan, J. / Lascu, I. / Janin, J.
History
DepositionMar 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)29,0432
Polymers29,0432
Non-polymers00
Water46826
1
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE

A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE

A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)87,1296
Polymers87,1296
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
Buried area10350 Å2
ΔGint-28.6 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.419, 108.419, 108.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-2006-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESI 2:43 OR RESI 65:136) AND (NAME C OR NAME O OR NAME CA OR NAME CB OR NAME N ))
211(CHAIN B AND (RESI 2:43 OR RESI 65:136) AND (NAME C OR NAME O OR NAME CA OR NAME CB OR NAME N ))

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Components

#1: Protein NUCLEOSIDE DIPHOSPHATE KINASE / NDK / NDKA / NDP KINASE / NUCLEOSIDE-2-P KINASE


Mass: 14521.485 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL
References: UniProt: P84284, UniProt: P9WJH7*PLUS, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 93 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 93 TO ASN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.4 % / Description: NONE
Crystal growpH: 7.5
Details: 2.0 M AMMONIUM SULFATE, 2% (V/V) PEG400, 0.1 M HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.81→26.3 Å / Num. obs: 10722 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 11 % / Biso Wilson estimate: 69.93 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.6
Reflection shellResolution: 2.81→2.95 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K44

1k44


Resolution: 2.808→26.295 Å / SU ML: 0.37 / σ(F): 0.11 / Phase error: 26.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2516 502 4.8 %
Rwork0.2199 --
obs0.2215 10557 99.29 %
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.715 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso mean: 74.83 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.808→26.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 0 26 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031985
X-RAY DIFFRACTIONf_angle_d0.7652696
X-RAY DIFFRACTIONf_dihedral_angle_d14.104710
X-RAY DIFFRACTIONf_chiral_restr0.046324
X-RAY DIFFRACTIONf_plane_restr0.003354
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A559X-RAY DIFFRACTIONPOSITIONAL
12B559X-RAY DIFFRACTIONPOSITIONAL0.02
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8078-3.090.41161110.34512437X-RAY DIFFRACTION97
3.09-3.53620.31021230.2492503X-RAY DIFFRACTION100
3.5362-4.45170.23361480.20562494X-RAY DIFFRACTION100
4.4517-26.29660.21471200.19352621X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.741.79050.46184.1027-0.76790.6633-0.1209-0.34950.0222-0.29260.1381-0.18960.1111-0.11580.00340.245-0.07640.12210.2982-0.10640.345826.58132.8836-10.6243
22.30841.8714-1.40128.38441.52491.99720.5218-0.6219-0.1842-0.7127-1.26280.8258-0.23280.82340.39020.3401-0.1437-0.12360.618-0.21440.463513.7257-2.4435-24.427
30.79911.7102-0.60472.4235-0.28432.3619-0.0120.22380.2797-0.17880.01210.50080.1458-0.69280.03880.2257-0.11320.05640.4371-0.10390.345922.68556.7325-16.71
42.94490.1615-1.74190.062-0.4532.8436-0.0714-0.1327-0.0745-0.2140.1702-0.03930.43490.07110.02230.3972-0.08950.14020.2663-0.05110.349933.8303-3.386-1.1889
50.4166-0.14370.9872.0148-0.68873.66470.43050.2033-0.1076-0.1328-0.34840.52091.20110.44610.25681.42540.06660.56630.75980.29580.778729.7291-8.07216.414
63.02361.5404-1.25862.4366-2.09951.6005-0.1039-0.3536-0.41220.7285-0.0166-0.15560.39340.14580.1990.5365-0.09720.13420.29850.05670.329938.4209-6.68854.7131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESI 2:43)
2X-RAY DIFFRACTION2(CHAIN A AND RESI 44:64)
3X-RAY DIFFRACTION3(CHAIN A AND RESI 65:136)
4X-RAY DIFFRACTION4(CHAIN B AND RESI 2:43)
5X-RAY DIFFRACTION5(CHAIN B AND RESI 44:64)
6X-RAY DIFFRACTION6(CHAIN B AND RESI 65:136)

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