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- PDB-3pj9: Crystal structure of a Nucleoside Diphosphate Kinase from Campylo... -

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Basic information

Entry
Database: PDB / ID: 3pj9
TitleCrystal structure of a Nucleoside Diphosphate Kinase from Campylobacter jejuni
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Nucleoside Diphosphate Kinase / Ndk / Campylobacter jejuni subsp. jejuni NCTC 11168
Function / homology
Function and homology information


nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / 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-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 speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Onopriyenko, O. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of a Nucleoside Diphosphate Kinase from Campylobacter jejuni
Authors: Filippova, E.V. / Wawrzak, Z. / Onopriyenko, O. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jun 27, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.4Sep 6, 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,89616
Polymers61,7434
Non-polymers1,15312
Water5,909328
1
A: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5449
Polymers30,8722
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-105 kcal/mol
Surface area13990 Å2
MethodPISA
2
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3527
Polymers30,8722
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-77 kcal/mol
Surface area13680 Å2
MethodPISA
3
A: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
hetero molecules

B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,89616
Polymers61,7434
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_646-x+1,y-1/2,-z+3/21
Buried area8190 Å2
ΔGint-199 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.672, 88.142, 110.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15435.769 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: Cj0332c, ndk / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q9PIG7, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2M NH4 Sulfate, 5% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2010 / Details: MIRROR
RadiationMonochromator: C(111) / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 49704 / Num. obs: 49704 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 22.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2433 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
CCP4model building
MrBUMPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NCK

2nck


Resolution: 2.1→28.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.143 / SU ML: 0.086 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19199 2511 5.1 %RANDOM
Rwork0.16956 ---
obs0.17072 46976 99.15 %-
all-46976 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.152 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.94 Å20 Å2
3----1.66 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4255 0 60 328 4643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224413
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9875929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51525.238189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4215845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8561521
X-RAY DIFFRACTIONr_chiral_restr0.110.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213217
X-RAY DIFFRACTIONr_mcbond_it0.8541.52755
X-RAY DIFFRACTIONr_mcangle_it1.55724431
X-RAY DIFFRACTIONr_scbond_it2.68431658
X-RAY DIFFRACTIONr_scangle_it4.414.51498
LS refinement shellResolution: 2.097→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 177 -
Rwork0.192 3233 -
obs--93.4 %
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)
12.8738-1.5467-0.3242.67780.1342.3891-0.198-0.0579-0.55150.24010.04580.51050.2891-0.19480.15220.1929-0.02190.08390.09110.00380.246335.773355.886773.4847
21.7721-0.30260.24341.7516-0.26232.3681-0.07360.166-0.0051-0.1501-0.0637-0.01870.055-0.09150.13730.1679-0.00720.01220.1457-0.03470.09923.736684.194783.4572
31.1562-0.10.41941.6045-0.763.3918-0.0308-0.1996-0.00870.1717-0.1021-0.1184-0.07390.27420.13290.14920.0042-0.03840.22270.03260.104726.788488.031652.3988
43.3653-1.15050.39832.5215-0.22293.15020.09690.46470.5536-0.1262-0.2554-0.4065-0.12680.48480.15850.10030.00910.0310.22110.12050.220352.589871.579561.6995
51.2053-1.1497-0.33451.7052-0.43821.5362-0.0383-0.0063-0.0374-0.08960.11340.13860.0445-0.0012-0.07510.0633-0.0572-0.02760.05550.02170.027536.287170.79967.5935
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 137
2X-RAY DIFFRACTION2B1 - 137
3X-RAY DIFFRACTION3C1 - 137
4X-RAY DIFFRACTION4D-1 - 137
5X-RAY DIFFRACTION5A - D1 - 140

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