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- PDB-2hf1: Crystal structure of the putative Tetraacyldisaccharide-1-P 4-kin... -

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Basic information

Entry
Database: PDB / ID: 2hf1
TitleCrystal structure of the putative Tetraacyldisaccharide-1-P 4-kinase from Chromobacterium violaceum. NESG target CvR39.
ComponentsTetraacyldisaccharide-1-P 4-kinase
KeywordsTRANSFERASE / Tetraacyldisaccharide-1-P 4-kinase / LpxK / lipid A biosynthesis / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyTrm112-like / Trm112p-like protein / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Single Sheet / Mainly Beta / cytosol / UPF0434 protein CV_3345
Function and homology information
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsVorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Chen, C.X. / Jiang, M. / Cunningham, K. / Ma, L.C. / Xiao, R. / Acton, T. / Montelione, G.T. ...Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Chen, C.X. / Jiang, M. / Cunningham, K. / Ma, L.C. / Xiao, R. / Acton, T. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the putative Tetraacyldisaccharide-1-P 4-kinase from Chromobacterium violaceum.
Authors: Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Chen, C.X. / Jiang, M. / Cunningham, K. / Ma, L.C. / Xiao, R. / Acton, T. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software / Item: _reflns_shell.percent_possible_all / _software.name
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetraacyldisaccharide-1-P 4-kinase
B: Tetraacyldisaccharide-1-P 4-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0754
Polymers15,9442
Non-polymers1312
Water93752
1
A: Tetraacyldisaccharide-1-P 4-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0372
Polymers7,9721
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tetraacyldisaccharide-1-P 4-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0372
Polymers7,9721
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-17 kcal/mol
Surface area6990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)27.517, 93.854, 87.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Tetraacyldisaccharide-1-P 4-kinase


Mass: 7971.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: ATCC 12472 / Gene: CV_3345 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
References: UniProt: Q7NSS5, tetraacyldisaccharide 4'-kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.76 Å3/Da / Density % sol: 30.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25-35% PEG 300, 0.1M sodium acetate, 5 mM ZnCl(2), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97907, 0.97940, 0.96791
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 8, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979071
20.97941
30.967911
ReflectionResolution: 1.9→31.9 Å / Num. all: 17246 / Num. obs: 17211 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 6.9 / Num. unique all: 1750

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Processing

Software
NameVersionClassification
CNS1.1refinement
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→26.41 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 163383.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 660 4.1 %RANDOM
Rwork0.233 ---
obs0.233 16173 93.9 %-
all-16176 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.2674 Å2 / ksol: 0.372862 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.93 Å20 Å20 Å2
2--0.64 Å20 Å2
3---2.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→26.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 0 2 52 979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 87 3.6 %
Rwork0.286 2312 -
obs--83.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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