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- PDB-3q8y: Crystal structure of Staphylococcus aureus nucleoside diphosphate... -

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Basic information

Entry
Database: PDB / ID: 3q8y
TitleCrystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with ADP and Vanadate
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Ferridoxin fold / alpha-beta protein family / Nucleoside diphosphate kinases (NDKs) / 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 / 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
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr1_label_seq_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)144,89126
Polymers141,3118
Non-polymers3,58018
Water2,198122
1
A: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2063
Polymers17,6641
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2304
Polymers17,6641
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7792
Polymers17,6641
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2304
Polymers17,6641
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2304
Polymers17,6641
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7792
Polymers17,6641
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2063
Polymers17,6641
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2304
Polymers17,6641
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.910, 71.367, 160.080
Angle α, β, γ (deg.)90.00, 108.04, 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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: VO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 298 K / Method: microbatch crystallization / pH: 8.5
Details: 0.1M Tris-Cl (pH 8.5), 20% PEG 3350, Microbatch Crystallization, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7355 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2010 / Details: Grazing angle 2.8 mrad
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7355 Å / Relative weight: 1
ReflectionResolution: 2.7→60.49 Å / Num. obs: 35635 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 67.6 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 5.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5175 / % possible all: 100

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Processing

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

3q83


Resolution: 2.7→51.67 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.896 / SU B: 36.282 / SU ML: 0.343 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27077 1777 5 %RANDOM
Rwork0.25077 ---
obs0.25181 33709 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.821 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0.03 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.397 Å
Refinement stepCycle: LAST / Resolution: 2.7→51.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9232 0 206 122 9560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229650
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.98513110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07351184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31923.832428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.531151604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.131572
X-RAY DIFFRACTIONr_chiral_restr0.0940.21448
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217250
X-RAY DIFFRACTIONr_mcbond_it0.5511.55912
X-RAY DIFFRACTIONr_mcangle_it1.08929539
X-RAY DIFFRACTIONr_scbond_it1.61233738
X-RAY DIFFRACTIONr_scangle_it2.8464.53571
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A580tight positional0.050.05
B580tight positional0.050.05
C580tight positional0.050.05
D580tight positional0.050.05
E580tight positional0.050.05
F580tight positional0.050.05
G580tight positional0.050.05
H580tight positional0.040.05
A543medium positional0.050.5
B543medium positional0.050.5
C543medium positional0.050.5
D543medium positional0.050.5
E543medium positional0.050.5
F543medium positional0.060.5
G543medium positional0.050.5
H543medium positional0.040.5
A580tight thermal0.090.5
B580tight thermal0.110.5
C580tight thermal0.090.5
D580tight thermal0.10.5
E580tight thermal0.10.5
F580tight thermal0.10.5
G580tight thermal0.10.5
H580tight thermal0.070.5
A543medium thermal0.12
B543medium thermal0.122
C543medium thermal0.12
D543medium thermal0.112
E543medium thermal0.12
F543medium thermal0.112
G543medium thermal0.12
H543medium thermal0.082
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 136 -
Rwork0.314 2473 -
obs--100 %
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)
11.83160.2772-1.14330.5091-0.97454.7779-0.03550.04440.06410.07820.1409-0.03850.42240.6531-0.10530.33840.116-0.11090.365-0.08240.164411.9369-13.91982.2686
21.0079-0.56490.74581.7097-0.6592.63880.03630.0120.28560.0743-0.1381-0.2383-0.04850.44310.10190.01360.00510.00790.2578-0.02150.25518.0515-0.6245-36.5566
32.7028-0.5103-0.2331.3653-0.49273.375-0.1158-0.00410.3836-0.0555-0.0737-0.3291-0.5273-0.09940.18950.25360.0377-0.00890.0894-0.00220.36474.212922.3931-55.2017
41.9991-0.203-0.03891.5316-0.50081.40780.0537-0.10640.22480.14280.00420.2452-0.1232-0.5408-0.05790.07420.06340.06410.4786-0.03190.1699-14.38163.9424-35.4038
50.4889-0.73070.42681.8595-0.74411.50980.2049-0.0816-0.0089-0.3396-0.03660.34090.5186-0.5981-0.16830.1965-0.1784-0.07940.41690.0140.2726-15.3409-14.1472-51.2272
61.77010.14-0.06551.3627-0.6362.56410.03580.1167-0.0437-0.5754-0.1156-0.28530.55620.5520.07980.31350.16790.14390.22340.02260.227216.9956-14.5633-56.412
71.016-0.25430.12052.6123-1.4111.4395-0.04740.0715-0.0005-0.60360.02380.04890.2678-0.1010.02360.32910.07310.03460.2675-0.00780.1332-2.2016.8869-72.4686
80.39820.05190.27430.25590.26713.04280.00140.1467-0.14660.05080.23940.05211.433-0.269-0.24081.2437-0.2575-0.15990.3419-0.01350.3086-5.757730.7967-20.1358
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 128
2X-RAY DIFFRACTION1A129 - 149
3X-RAY DIFFRACTION2B1 - 128
4X-RAY DIFFRACTION2B129 - 149
5X-RAY DIFFRACTION3C1 - 128
6X-RAY DIFFRACTION3C129 - 149
7X-RAY DIFFRACTION4D1 - 128
8X-RAY DIFFRACTION4D129 - 149
9X-RAY DIFFRACTION5E1 - 128
10X-RAY DIFFRACTION5E129 - 149
11X-RAY DIFFRACTION6F1 - 128
12X-RAY DIFFRACTION6F129 - 149
13X-RAY DIFFRACTION7G1 - 128
14X-RAY DIFFRACTION7G129 - 149
15X-RAY DIFFRACTION8H1 - 128
16X-RAY DIFFRACTION8H129 - 149

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