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- PDB-3q83: Crystal structure of Staphylococcus aureus nucleoside diphosphate... -

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Basic information

Entry
Database: PDB / ID: 3q83
TitleCrystal structure of Staphylococcus aureus nucleoside diphosphate kinase
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Ferridoxin fold / alpha-beta protein family / Nucleoside diphosphate kinases (NDKs) catalyze the transfer of a gamma phosphate from nucleoside triphosphates to nucleoside diphosphate / Nucleotide binding / Metal binding / Phosphorylation / Kinase / Nucleotide metabolism
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / 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 ...Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / 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
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSrivastava, S.K. / Rajasree, K. / Gopal, B.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase.
Authors: Srivastava, S.K. / Rajasree, K. / Gopal, B.
History
DepositionJan 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)105,9836
Polymers105,9836
Non-polymers00
Water7,728429
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)52,9923
Polymers52,9923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-18 kcal/mol
Surface area18790 Å2
MethodPISA
2
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)52,9923
Polymers52,9923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-16 kcal/mol
Surface area19060 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17130 Å2
ΔGint-72 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.615, 91.615, 176.876
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 1 - 149 / Label seq-ID: 1 - 149

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

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


Mass: 17663.873 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: genomic DNA
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: COL / Gene: ndk, SACOL1509 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HFV4, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 298 K / Method: micobatch crystallization / pH: 4.6
Details: 0.1M MgCl2, 0.1M Na-Acetate, pH 4.6, 20% PEG 2000, Micobatch Crystallization, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2009 / Details: Grazing angle 2.8 mrad
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→72.36 Å / Num. obs: 30434 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 7.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4378 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JXV

1jxv


Resolution: 2.5→45.81 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.846 / SU B: 10.569 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26863 1533 5 %RANDOM
Rwork0.21252 ---
obs0.21537 28887 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.345 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6936 0 0 429 7365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227074
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9589579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90223.944322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7151208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8961553
X-RAY DIFFRACTIONr_chiral_restr0.1210.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215368
X-RAY DIFFRACTIONr_mcbond_it0.5651.54429
X-RAY DIFFRACTIONr_mcangle_it1.11627145
X-RAY DIFFRACTIONr_scbond_it1.75732645
X-RAY DIFFRACTIONr_scangle_it2.9234.52434
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A540tight positional0.050.05
B540tight positional0.070.05
C540tight positional0.060.05
D540tight positional0.060.05
E540tight positional0.050.05
F540tight positional0.070.05
A505medium positional0.060.5
B505medium positional0.080.5
C505medium positional0.060.5
D505medium positional0.070.5
E505medium positional0.060.5
F505medium positional0.070.5
A540tight thermal0.120.5
B540tight thermal0.130.5
C540tight thermal0.120.5
D540tight thermal0.120.5
E540tight thermal0.120.5
F540tight thermal0.140.5
A505medium thermal0.132
B505medium thermal0.142
C505medium thermal0.132
D505medium thermal0.132
E505medium thermal0.132
F505medium thermal0.142
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 111 -
Rwork0.26 2097 -
obs--100 %

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