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- PDB-6qa2: R80A MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM T... -

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Basic information

Entry
Database: PDB / ID: 6qa2
TitleR80A MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsNucleoside diphosphate kinaseNucleoside-diphosphate kinase
KeywordsTRANSFERASE / Remodeling / Open and closed binding site
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase-like domain / 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
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDautant, A. / Henri, J. / Wales, T.E. / Meyer, P. / Engen, J.R. / Georgescauld, F.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-024 France
French National Research AgencyANR-11-LABX-0011-01 France
Fondation ARCSFI20101201793 France
Citation
Journal: Biochemistry / Year: 2019
Title: Remodeling of the Binding Site of Nucleoside Diphosphate Kinase Revealed by X-ray Structure and H/D Exchange.
Authors: Dautant, A. / Henri, J. / Wales, T.E. / Meyer, P. / Engen, J.R. / Georgescauld, F.
#1: Journal: Biochemistry / Year: 2017
Title: Hydrogen/Deuterium Exchange Mass Spectrometry Reveals Mechanistic Details of Activation of Nucleoside Diphosphate Kinases by Oligomerization.
Authors: Dautant, A. / Meyer, P. / Georgescauld, F.
History
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,09720
Polymers86,6186
Non-polymers1,47914
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13350 Å2
ΔGint-156 kcal/mol
Surface area30020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.107, 121.730, 150.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11E-305-

HOH

21E-347-

HOH

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Components

#1: Protein
Nucleoside diphosphate kinase / Nucleoside-diphosphate kinase / NDP kinase / Nucleoside-2-P kinase


Mass: 14436.353 Da / Num. of mol.: 6 / Mutation: R80A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: ndk, MRA_2471 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: A5U5E1, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.84 % / Description: Platelets
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.8 M ammonium sulfate, 0.1 M HEPES-NaOH, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.961 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 23, 2018 / Details: NULL
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.961 Å / Relative weight: 1
ReflectionResolution: 2.2→34.3 Å / Num. obs: 52205 / % possible obs: 98.1 % / Redundancy: 7.4 % / Biso Wilson estimate: 25.65 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.054 / Rrim(I) all: 0.152 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 7546 / Rpim(I) all: 0.299 / Rrim(I) all: 0.843 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMv7.2.1data reduction
SCALAv3.3.22data scaling
MOLREPv11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ANE
Resolution: 2.2→34.067 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.86
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2475 4.74 %RANDOM
Rwork0.186 ---
obs0.186 52182 98.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5717 0 82 467 6266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025871
X-RAY DIFFRACTIONf_angle_d0.497975
X-RAY DIFFRACTIONf_dihedral_angle_d14.4653488
X-RAY DIFFRACTIONf_chiral_restr0.043942
X-RAY DIFFRACTIONf_plane_restr0.0031033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.24230.32731170.2912766X-RAY DIFFRACTION99
2.2423-2.28810.38421190.32752728X-RAY DIFFRACTION99
2.2881-2.33780.29161160.23132773X-RAY DIFFRACTION99
2.3378-2.39220.24421270.20772759X-RAY DIFFRACTION99
2.3922-2.4520.27311280.20722741X-RAY DIFFRACTION99
2.452-2.51830.21891510.19462719X-RAY DIFFRACTION99
2.5183-2.59230.241300.19272719X-RAY DIFFRACTION98
2.5923-2.6760.22321180.18812728X-RAY DIFFRACTION97
2.676-2.77160.22531330.19562635X-RAY DIFFRACTION95
2.7716-2.88250.24241230.19572576X-RAY DIFFRACTION93
2.8825-3.01360.25961380.19492741X-RAY DIFFRACTION98
3.0136-3.17240.21211330.18692795X-RAY DIFFRACTION100
3.1724-3.3710.2191720.17582778X-RAY DIFFRACTION100
3.371-3.6310.19271430.16152813X-RAY DIFFRACTION100
3.631-3.99590.1661480.14942816X-RAY DIFFRACTION100
3.9959-4.57290.16421570.12982805X-RAY DIFFRACTION100
4.5729-5.75690.15281700.14032838X-RAY DIFFRACTION100
5.7569-34.07130.21081520.18862977X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.43512.22040.31316.42853.43196.14910.0632-0.0911-0.4213-0.0502-0.07030.61550.3722-0.8151-0.08020.1928-0.0226-0.02830.20920.06490.39465.030328.61429.8254
29.21645.2273-3.99293.4014-3.30045.60680.0088-0.5594-0.47830.7443-0.3066-0.87390.0820.6150.29050.2853-0.0127-0.02950.26920.10490.3520.219329.835340.2757
33.6733-2.77711.16382.72850.85146.86820.11060.33470.2625-0.1025-0.10160.0042-0.17790.1032-0.03770.1852-0.0437-0.0060.21720.06990.237910.541235.935232.9141
46.65512.72840.34265.76811.89687.16570.4038-0.5668-0.81830.5868-0.52350.81870.781-0.68560.07840.2619-0.08210.00350.31540.07680.50856.677617.566743.0481
54.2791-5.7525-0.84059.4643.49194.19430.0333-0.1499-0.1696-0.6507-0.2932-1.0660.0718-0.04160.27140.30180.00460.03840.36420.11320.702412.56749.787534.7738
62.25180.8703-0.78563.391-1.97676.46350.00960.0454-0.203-0.02740.03330.10060.20280.0555-0.0410.1208-0.05890.00930.19920.01660.2311.479824.681333.6195
77.31692.1699-4.24716.9616-0.97998.4586-0.13190.2964-0.508-0.10030.0505-0.1490.3681-0.06770.04880.1567-0.0211-0.02170.20040.02950.223724.17625.290428.443
85.13272.27565.01441.17492.34084.98230.9668-0.7607-1.59530.2537-0.5976-0.77440.818-0.834-0.4190.2676-0.0988-0.00150.3158-0.01190.370512.832423.498430.0149
99.16151.5846-2.04085.45612.24299.2778-0.38960.1635-0.6656-0.2025-0.18650.33410.5983-0.55380.53110.2146-0.0586-00.28340.05980.40720.598522.455933.3664
105.93272.77351.06856.37070.8883.18870.1677-0.8035-0.47740.74770.09320.46990.5387-0.6083-0.21510.30920.01140.14610.32170.05350.234511.628643.731450.9461
113.7473-4.5428-5.47218.47624.57749.41520.1250.6974-0.082-0.9162-0.54131.4436-0.5505-0.84140.43280.29410.0581-0.05890.33950.01560.50075.221647.817233.8738
121.70210.58371.90664.0817-0.83455.59410.08550.13280.1610.0835-0.14780.0167-0.01910.1270.08660.16470.00120.02090.1604-0.00380.19512.600941.403141.863
135.2807-3.846-0.18024.9006-0.9834.0526-0.1889-0.78581.1160.54280.08981.3194-0.7015-2.0750.21280.45690.12160.2140.7607-0.02940.996-5.068949.941648.567
145.93225.79665.27895.66385.11097.9660.1925-0.1345-0.25930.1779-0.0111-0.03470.5028-0.5134-0.20480.1429-0.06330.08950.2638-0.00360.19947.380941.476945.3857
153.9266-1.55953.93946.2734-5.85588.46310.13460.01490.3450.3011-0.03940.3336-0.19550.0691-0.11330.1901-0.0170.07530.24920.00650.304315.537555.043643.2111
169.9026-3.52123.65822.9288-0.80085.0193-0.16770.46660.6387-0.2399-0.171.3525-0.7871-1.35150.25770.30840.0968-0.02340.4380.02430.62374.704658.824836.239
176.5-3.16154.66924.3494-3.84774.7539-0.2061-0.47710.72020.6381-0.02920.4287-0.488-1.40460.2370.2856-0.03020.1070.3173-0.08040.38818.593251.725647.2886
188.3096.48113.10097.01270.09814.49980.3333-1.08860.53620.9854-0.31910.7902-0.0265-0.82470.04390.3519-0.02810.18340.61490.04790.45764.597842.748855.4763
196.5885-1.12520.7824.3898-0.18765.0575-0.01070.53150.2889-0.18180.0315-0.4178-0.04210.1443-0.00950.12220.00210.01540.30450.04860.218841.659937.655224.5974
202.97012.0529-1.75982.43990.07523.3710.1038-0.04410.0686-0.0991-0.092-0.27670.12260.3222-0.02530.20650.0606-0.01260.28070.09740.331243.475836.691827.9664
219.1381-5.5674-4.47783.95493.52193.34650.63961.9132-0.0564-2.1244-1.1080.3135-0.4596-1.04160.42740.80020.1833-0.14940.7875-0.01050.701853.52628.752211.748
224.1119-4.4863-5.41334.98685.77559.45810.57892.1494-0.0833-1.8222-0.65570.4915-0.10340.95530.08410.71770.2091-0.00931.07930.11820.629952.15437.016610.9737
235.50121.27941.86763.07262.12921.66860.2743-0.1536-0.04260.2385-0.3661-0.5085-0.04940.27430.12120.13620.0593-0.01480.21370.06310.27744.100534.874627.8727
241.25321.7257-0.58326.9722-2.50737.69910.04360.419-0.0485-0.4295-0.1008-0.44490.13010.21960.04250.1950.0350.04490.30630.03740.236735.353133.908417.295
258.4386.34773.8035.03933.49775.26430.48090.5319-1.13360.20050.1625-0.94530.56690.6568-0.64650.27280.0688-0.0840.3713-0.05130.477850.345926.716827.6879
267.26913.9605-1.74963.25851.51725.97380.0820.50630.5929-0.3394-0.2307-0.7776-0.38230.64980.18790.19610.01230.0230.32220.09830.48244.964954.215937.6604
273.87833.08843.93796.59044.92455.03530.0807-0.7608-0.85371.0579-0.36560.48021.431-0.34140.16980.43430.05070.13490.35950.10950.440934.418139.988543.5577
287.7558-3.20252.63486.118-2.0086.55220.25310.0890.0251-0.0975-0.0539-0.0416-0.00720.0852-0.21230.1359-0.00160.02050.12750.02060.251439.684647.219934.4612
294.08825.22250.05599.10990.68311.75110.0426-2.3323-0.08244.59970.2245-2.07390.03480.3163-0.20481.00070.1293-0.23060.8986-0.01050.761150.652846.839554.8676
306.5842-5.3334-2.08749.36412.20698.1683-0.1478-0.4112-0.71581.1993-0.4342-0.22330.257-0.08070.53190.4111-0.0513-0.0550.50980.10750.442145.708246.065850.9507
313.4505-0.1755-2.0581.27340.87963.62620.1337-0.2090.14640.1687-0.0128-0.2-0.02550.098-0.11970.1773-0.0205-0.05820.18610.05350.301334.885952.304743.6694
325.8315-4.4135-1.69883.42240.80474.4044-0.0126-0.88610.660.17060.0023-0.8831-0.33830.9792-0.06730.2338-0.0551-0.01560.47470.07070.504551.977353.50142.0914
331.90980.3083-2.06885.0736-1.8368.14710.03120.72110.6442-0.15410.29860.4057-0.1893-0.5795-0.39460.2786-0.0145-0.03450.41520.16780.306515.695648.920611.0868
341.2131-1.0586-0.08592.942-0.74131.776-0.04980.74230.1158-0.46160.19160.4054-0.0441-0.40020.02190.40990.0083-0.02290.5940.23840.343217.605951.85759.2645
353.70354.24861.26665.34283.2617.4715-0.44340.3825-0.0451-0.03160.20621.1731.5704-1.43730.22340.7859-0.1395-0.06840.94470.35830.81944.860446.5061.9815
360.1537-0.59270.40772.2648-1.44052.5879-0.02260.47660.127-0.47350.06550.07650.1331-0.2393-0.08020.3393-0.0096-0.01920.49030.14370.255817.75543.39267.5331
374.0478-1.304-1.21112.5769-0.74242.5475-0.1375-0.08020.03920.44260.30740.4765-0.4115-0.4963-0.33940.42580.20660.12750.45560.27310.456713.872567.315122.0111
388.97375.5502-0.64289.2051-0.58446.8778-0.17670.8855-0.2288-0.55250.3797-1.5728-0.02221.2384-0.16620.2760.03410.08920.60090.07970.490330.803159.927719.0266
392.2453-0.3219-0.49481.43270.57055.6039-0.0040.2474-0.0267-0.19870.21210.18640.059-0.3326-0.20970.2450.03850.00620.34780.17280.300618.107959.032420.0991
405.3703-0.42981.49960.04420.05643.73250.02220.56891.643-0.89410.1854-0.298-1.82270.2888-0.01030.91820.00350.1380.45190.25920.876626.814276.941115.2886
410.0243-0.25890.32433.7196-2.58285.09010.04390.10750.0942-0.10590.04320.039-0.1786-0.2354-0.40910.39240.11690.1030.46070.26760.377117.636464.506617.577
421.4392-1.2510.83481.51520.00781.76870.16160.17830.6999-0.06080.0918-0.2886-0.425-0.1531-0.16790.32490.04180.08090.25530.13580.421425.154865.505630.0256
430.378-0.32080.79991.2411-1.18682.0341-0.14910.02020.14830.2198-0.0335-0.1541-0.4659-0.0564-0.07350.50660.2040.08610.64230.48620.65113.694873.922516.8709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 18 )
3X-RAY DIFFRACTION3chain 'A' and (resid 19 through 39 )
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 49 )
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 58 )
6X-RAY DIFFRACTION6chain 'A' and (resid 59 through 89 )
7X-RAY DIFFRACTION7chain 'A' and (resid 90 through 113 )
8X-RAY DIFFRACTION8chain 'A' and (resid 114 through 121 )
9X-RAY DIFFRACTION9chain 'A' and (resid 122 through 136 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 9 )
11X-RAY DIFFRACTION11chain 'B' and (resid 10 through 18 )
12X-RAY DIFFRACTION12chain 'B' and (resid 19 through 41 )
13X-RAY DIFFRACTION13chain 'B' and (resid 42 through 68 )
14X-RAY DIFFRACTION14chain 'B' and (resid 69 through 77 )
15X-RAY DIFFRACTION15chain 'B' and (resid 78 through 107 )
16X-RAY DIFFRACTION16chain 'B' and (resid 108 through 113 )
17X-RAY DIFFRACTION17chain 'B' and (resid 114 through 121 )
18X-RAY DIFFRACTION18chain 'B' and (resid 122 through 136 )
19X-RAY DIFFRACTION19chain 'C' and (resid 2 through 18 )
20X-RAY DIFFRACTION20chain 'C' and (resid 19 through 49 )
21X-RAY DIFFRACTION21chain 'C' and (resid 50 through 56 )
22X-RAY DIFFRACTION22chain 'C' and (resid 57 through 66 )
23X-RAY DIFFRACTION23chain 'C' and (resid 67 through 80 )
24X-RAY DIFFRACTION24chain 'C' and (resid 81 through 121 )
25X-RAY DIFFRACTION25chain 'C' and (resid 122 through 136 )
26X-RAY DIFFRACTION26chain 'D' and (resid 2 through 9 )
27X-RAY DIFFRACTION27chain 'D' and (resid 10 through 18 )
28X-RAY DIFFRACTION28chain 'D' and (resid 19 through 41 )
29X-RAY DIFFRACTION29chain 'D' and (resid 42 through 61 )
30X-RAY DIFFRACTION30chain 'D' and (resid 62 through 68 )
31X-RAY DIFFRACTION31chain 'D' and (resid 69 through 121 )
32X-RAY DIFFRACTION32chain 'D' and (resid 122 through 136 )
33X-RAY DIFFRACTION33chain 'E' and (resid 2 through 18 )
34X-RAY DIFFRACTION34chain 'E' and (resid 19 through 49 )
35X-RAY DIFFRACTION35chain 'E' and (resid 50 through 70 )
36X-RAY DIFFRACTION36chain 'E' and (resid 71 through 136 )
37X-RAY DIFFRACTION37chain 'F' and (resid 2 through 9 )
38X-RAY DIFFRACTION38chain 'F' and (resid 10 through 18 )
39X-RAY DIFFRACTION39chain 'F' and (resid 19 through 41 )
40X-RAY DIFFRACTION40chain 'F' and (resid 42 through 68 )
41X-RAY DIFFRACTION41chain 'F' and (resid 69 through 78 )
42X-RAY DIFFRACTION42chain 'F' and (resid 79 through 121 )
43X-RAY DIFFRACTION43chain 'F' and (resid 122 through 136 )

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