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- PDB-3q8v: Crystal structure of Staphylococcus aureus nucleoside diphosphate... -

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Basic information

Entry
Database: PDB / ID: 3q8v
TitleCrystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with UDP
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Ferridoxin fold / alpha-beta protein family / Nucleoside diphosphate kinases (NDKs) / a gamma phosphate / nucleoside triphosphates / nucleoside diphosphate / Nucleotide binding / Magnesium / Metal binding / Phosphorylation
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 (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / 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
URIDINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / 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 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,59614
Polymers141,3118
Non-polymers1,2856
Water3,801211
1
A: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0923
Polymers17,6641
Non-polymers4282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0923
Polymers17,6641
Non-polymers4282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)17,6641
Polymers17,6641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0923
Polymers17,6641
Non-polymers4282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)17,6641
Polymers17,6641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)17,6641
Polymers17,6641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)17,6641
Polymers17,6641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)17,6641
Polymers17,6641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.665, 72.916, 102.144
Angle α, β, γ (deg.)90.00, 108.42, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

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
7GG
8HH

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Components

#1: Protein
Nucleoside diphosphate kinase


Mass: 17663.873 Da / Num. of mol.: 8
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: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 298 K / Method: microbatch crystallization / pH: 7.2
Details: 0.1M Bis-Tris, pH 7.2, 30% PEG 3350, Microbatch Crystallization , temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 2010 / Details: VariMax
RadiationMonochromator: CuK (Alpha) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→34.12 Å / Num. obs: 45083 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 4.8 / Num. unique all: 6465 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q83

3q83


Resolution: 2.5→32.3 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.857 / SU B: 21.514 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28286 2268 5 %RANDOM
Rwork0.23031 ---
obs0.23296 42809 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.304 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.339 Å
Refinement stepCycle: LAST / Resolution: 2.5→32.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9159 0 78 211 9448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229423
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.96512773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33851184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12423.795419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.964151574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.661572
X-RAY DIFFRACTIONr_chiral_restr0.1070.21422
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217124
X-RAY DIFFRACTIONr_mcbond_it0.5811.55900
X-RAY DIFFRACTIONr_mcangle_it1.10929477
X-RAY DIFFRACTIONr_scbond_it1.833523
X-RAY DIFFRACTIONr_scangle_it3.0644.53296
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A512tight positional0.060.05
B512tight positional0.090.05
C512tight positional0.060.05
D512tight positional0.060.05
E512tight positional0.060.05
F512tight positional0.050.05
G512tight positional0.060.05
H512tight positional0.060.05
A475medium positional0.060.5
B475medium positional0.080.5
C475medium positional0.060.5
D475medium positional0.060.5
E475medium positional0.060.5
F475medium positional0.050.5
G475medium positional0.060.5
H475medium positional0.060.5
A512tight thermal0.180.5
B512tight thermal0.220.5
C512tight thermal0.150.5
D512tight thermal0.140.5
E512tight thermal0.150.5
F512tight thermal0.120.5
G512tight thermal0.130.5
H512tight thermal0.140.5
A475medium thermal0.182
B475medium thermal0.192
C475medium thermal0.162
D475medium thermal0.152
E475medium thermal0.172
F475medium thermal0.142
G475medium thermal0.132
H475medium thermal0.132
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 184 -
Rwork0.238 3085 -
obs--98.82 %
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)
11.73090.05860.3771.00340.06260.7406-0.02540.01570.2589-0.01370.03930.2473-0.07880.0831-0.01390.1175-0.01870.01450.01170.00070.210420.1317-4.33675.547
22.4407-0.0751-0.03451.15940.26120.43830.02020.1324-0.0802-0.07240.0059-0.0351-0.04910.062-0.02610.07960.02350.00890.0739-0.03350.040340.9892-28.68150.4702
31.52310.23330.00571.3151-0.02641.19360.0096-0.138-0.34980.06560.01580.25110.11630.0294-0.02530.11350.0174-0.0180.02660.00570.249623.621-42.96999.313
41.38080.0219-0.02551.39570.22131.00170.0755-0.27790.18860.251-0.0655-0.0391-0.09730.1426-0.00990.1956-0.0598-0.04260.226-0.06380.05943.2235-10.906827.5116
51.67890.01630.45261.12850.31231.19080.025-0.37610.11730.261-0.03880.37070.005-0.15740.01380.0968-0.01570.10040.1376-0.03780.27315.6524-17.613219.3284
61.7462-0.37940.5241.2730.33130.91830.0278-0.4608-0.13560.414-0.05410.14220.1243-0.08980.02630.3412-0.04980.04560.34280.07390.047230.1931-28.393237.9071
71.6304-0.00940.53080.9716-0.28582.3799-0.33340.2308-0.3115-0.20660.1130.18460.2584-0.22780.22050.2993-0.10810.10110.4231-0.05210.297467.1708-35.758241.9382
80.9330.0161-0.63112.49860.10351.1708-0.06210.27340.2464-0.3713-0.04210.1161-0.3193-0.30960.10420.393-0.0354-0.2010.43760.05850.313273.2153-6.464329.397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 87
2X-RAY DIFFRACTION1A88 - 149
3X-RAY DIFFRACTION2B1 - 87
4X-RAY DIFFRACTION2B88 - 149
5X-RAY DIFFRACTION3C1 - 85
6X-RAY DIFFRACTION3C86 - 149
7X-RAY DIFFRACTION4D1 - 85
8X-RAY DIFFRACTION4D86 - 149
9X-RAY DIFFRACTION5E1 - 87
10X-RAY DIFFRACTION5E88 - 149
11X-RAY DIFFRACTION6F1 - 87
12X-RAY DIFFRACTION6F88 - 149
13X-RAY DIFFRACTION7G1 - 85
14X-RAY DIFFRACTION7G86 - 149
15X-RAY DIFFRACTION8H1 - 85
16X-RAY DIFFRACTION8H86 - 149

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