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- PDB-4s0m: Crystal Structure of nucleoside diphosphate kinase at 1.92 A reso... -

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Basic information

Entry
Database: PDB / ID: 4s0m
TitleCrystal Structure of nucleoside diphosphate kinase at 1.92 A resolution from acinetobacter baumannii
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Kinase
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 speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.922 Å
AuthorsSikarwar, J. / Shukla, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal Structure of nucleoside diphosphate kinase at 1.92 A resolution from Acinetobacter baumannii
Authors: Sikarwar, J. / Shukla, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionJan 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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_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.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_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
F: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
I: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,91610
Polymers123,8688
Non-polymers492
Water15,241846
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,9672
Polymers30,9672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-14 kcal/mol
Surface area12930 Å2
MethodPISA
2
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9913
Polymers30,9672
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-18 kcal/mol
Surface area12930 Å2
MethodPISA
3
F: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9913
Polymers30,9672
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-12 kcal/mol
Surface area12890 Å2
MethodPISA
4
H: Nucleoside diphosphate kinase
I: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)30,9672
Polymers30,9672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-17 kcal/mol
Surface area12850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.924, 71.381, 129.427
Angle α, β, γ (deg.)90.00, 93.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15483.479 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC 19606
Gene: ABBL099_02780, BL01_17035, FL75_03050, FL80_07750, GQ86_04945, IOMTU433_3298, IX87_17090, LX00_02580, ndk, P795_14800
Plasmid: PET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: V5VIC4, nucleoside-diphosphate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.56 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG4000, 0.2 M AMMONIUM ACETATE,MgCl2, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 14, 2014 / Details: mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 93429 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071 / Net I/σ(I): 36.9
Reflection shellResolution: 1.92→1.94 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VGU

3vgu


Resolution: 1.922→31.679 Å / SU ML: 0.25 / σ(F): 1.33 / σ(I): 0 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 4639 5.04 %
Rwork0.2111 --
obs0.2135 92084 96.29 %
all-93429 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.922→31.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8704 0 2 846 9552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088853
X-RAY DIFFRACTIONf_angle_d1.12511944
X-RAY DIFFRACTIONf_dihedral_angle_d14.7193220
X-RAY DIFFRACTIONf_chiral_restr0.0521336
X-RAY DIFFRACTIONf_plane_restr0.0061584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9216-1.94340.46561140.45542148X-RAY DIFFRACTION72
1.9434-1.96630.55451560.51072856X-RAY DIFFRACTION95
1.9663-1.99020.42061510.31033003X-RAY DIFFRACTION99
1.9902-2.01540.30581650.2432990X-RAY DIFFRACTION100
2.0154-2.04190.28491520.22923026X-RAY DIFFRACTION100
2.0419-2.06990.28861550.22793018X-RAY DIFFRACTION100
2.0699-2.09950.26951440.23043049X-RAY DIFFRACTION100
2.0995-2.13080.27351630.22572953X-RAY DIFFRACTION100
2.1308-2.16410.28821660.22053066X-RAY DIFFRACTION100
2.1641-2.19960.35791670.28322852X-RAY DIFFRACTION97
2.1996-2.23750.34521420.34352748X-RAY DIFFRACTION90
2.2375-2.27820.45131470.40882989X-RAY DIFFRACTION99
2.2782-2.3220.48491360.3552506X-RAY DIFFRACTION84
2.322-2.36940.30111520.24583018X-RAY DIFFRACTION99
2.3694-2.42090.31021620.22463006X-RAY DIFFRACTION100
2.4209-2.47710.30171600.22043010X-RAY DIFFRACTION100
2.4771-2.53910.26851490.21833027X-RAY DIFFRACTION100
2.5391-2.60770.26121660.20952996X-RAY DIFFRACTION100
2.6077-2.68440.28651550.21293017X-RAY DIFFRACTION100
2.6844-2.7710.29131920.21452998X-RAY DIFFRACTION100
2.771-2.870.25071640.2052998X-RAY DIFFRACTION99
2.87-2.98480.23751560.20323015X-RAY DIFFRACTION100
2.9848-3.12050.26721680.20742987X-RAY DIFFRACTION100
3.1205-3.28490.24761530.19043039X-RAY DIFFRACTION100
3.2849-3.49040.23211740.18182991X-RAY DIFFRACTION99
3.4904-3.75950.22641530.18052754X-RAY DIFFRACTION91
3.7595-4.13710.16951310.162195X-RAY DIFFRACTION72
4.1371-4.73410.20981430.15713053X-RAY DIFFRACTION99
4.7341-5.9580.21791620.18313070X-RAY DIFFRACTION100
5.958-31.68360.21541410.18863067X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 15.2699 Å / Origin y: -9.7269 Å / Origin z: 32.1569 Å
111213212223313233
T0.1993 Å20.0001 Å2-0.0085 Å2-0.2455 Å20.0276 Å2--0.2775 Å2
L0.0074 °20.0059 °2-0.0864 °2-0.1838 °20.353 °2--1.3118 °2
S0.0077 Å °0.025 Å °0.0219 Å °0.0161 Å °0.003 Å °-0.0081 Å °0.0442 Å °-0.0621 Å °-0.0099 Å °
Refinement TLS groupSelection details: all

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