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- PDB-3q86: Crystal structure of Staphylococcus aureus nucleoside diphosphate... -

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Basic information

Entry
Database: PDB / ID: 3q86
TitleCrystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with GTP
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Ferridoxin fold / alpha-beta protein family / Nucleoside diphosphate kinases (NDKs) / transfer / 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 / 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
GUANOSINE-5'-TRIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 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 ...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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4236
Polymers35,3282
Non-polymers1,0954
Water2,432135
1
A: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6349
Polymers52,9923
Non-polymers1,6426
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5420 Å2
ΔGint-20 kcal/mol
Surface area18450 Å2
MethodPISA
2
B: Nucleoside diphosphate kinase
hetero molecules

B: Nucleoside diphosphate kinase
hetero molecules

B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6349
Polymers52,9923
Non-polymers1,6426
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5450 Å2
ΔGint-19 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.302, 75.302, 154.712
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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

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Components

#1: Protein Nucleoside diphosphate kinase


Mass: 17663.873 Da / Num. of mol.: 2
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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 298 K / Method: microbatch crystallization / pH: 5
Details: 0.1M Mgacetate, 0.1M citric acid, pH 5, 14% PEG 8000 , Microbatch Crystallization, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 5, 2010 / Details: Goebel Mirrors
RadiationMonochromator: CuK (Alpha) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.36→37.65 Å / Num. obs: 13104 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 46.4
Reflection shellResolution: 2.36→2.48 Å / Redundancy: 7 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 20.4 / Num. unique all: 1550 / % possible all: 78.5

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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: 2.38→37.65 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.553 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22011 644 4.9 %RANDOM
Rwork0.16626 ---
obs0.16877 12456 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.665 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.239 Å
Refinement stepCycle: LAST / Resolution: 2.38→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 66 135 2491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222428
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9923302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9835296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88823.889108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84215404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7881518
X-RAY DIFFRACTIONr_chiral_restr0.1260.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211816
X-RAY DIFFRACTIONr_mcbond_it0.7941.51476
X-RAY DIFFRACTIONr_mcangle_it1.55522378
X-RAY DIFFRACTIONr_scbond_it2.7823952
X-RAY DIFFRACTIONr_scangle_it4.6784.5924
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A580tight positional0.070.05
A549medium positional0.090.5
B580tight thermal0.210.5
B549medium thermal0.222
LS refinement shellResolution: 2.377→2.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 56 -
Rwork0.175 822 -
obs--93.8 %

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