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- PDB-4anc: CRYSTAL FORM I OF THE D93N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINAS... -

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Basic information

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


purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / 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 ...purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / 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 / cytosol / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase / 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: 2.8 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


Theoretical massNumber of molelcules
Total (without water)14,5211
Polymers14,5211
Non-polymers00
Water34219
1
A: NUCLEOSIDE DIPHOSPHATE KINASE
x 6


Theoretical massNumber of molelcules
Total (without water)87,1296
Polymers87,1296
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
crystal symmetry operation14_555-y+1/4,-x+1/4,-z+1/41
crystal symmetry operation22_455z-1/4,-y+3/4,x+1/41
crystal symmetry operation18_454-x-1/4,z+1/4,y-1/41
Buried area10100 Å2
ΔGint-38.1 kcal/mol
Surface area32740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.679, 110.679, 110.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-2013-

HOH

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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.: 1 / 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.: 19 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, 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: 3.93 Å3/Da / Density % sol: 68.5 % / Description: NONE
Crystal growpH: 8.5 / Details: 2.0 M AMMONIUM SULFATE, 0.1 M TRIS-HCL, PH 8.5

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Data collection

DiffractionMean temperature: 107 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: 2.8→26.9 Å / Num. obs: 6145 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 20.5 % / Biso Wilson estimate: 58.24 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 31.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 21 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 7.3 / % 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: 2.8→26.844 Å / SU ML: 0.36 / σ(F): 1.43 / Phase error: 24.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 281 4.6 %
Rwork0.2135 --
obs0.2144 6100 99.88 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.685 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso mean: 65.83 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→26.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 0 19 1010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021005
X-RAY DIFFRACTIONf_angle_d0.6531366
X-RAY DIFFRACTIONf_dihedral_angle_d12.182358
X-RAY DIFFRACTIONf_chiral_restr0.039164
X-RAY DIFFRACTIONf_plane_restr0.002180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-3.08190.33671290.29912562X-RAY DIFFRACTION100
3.0819-3.5270.24881160.23352589X-RAY DIFFRACTION100
3.527-4.44040.2351180.18982562X-RAY DIFFRACTION100
4.4404-26.84480.19641320.19912579X-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)
10.70120.49120.26690.35420.02532.6627-0.0045-0.0027-0.13290.1437-0.0267-0.1998-0.4506-0.0760.03930.32140.0031-0.12250.204-0.07070.2822.154946.271923.0853
21.53851.47421.88411.69872.41463.60470.41340.0565-0.4181-0.33310.27160.2036-0.2760.3462-0.68130.3537-0.19310.02990.1085-0.12330.374711.516262.47527.8471
33.13740.70651.93040.41630.91552.0934-0.14160.22860.54540.1380.1281-0.4247-0.18860.23140.0250.1259-0.0513-0.12040.0483-0.03970.31055.693552.313718.8487
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)

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