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- PDB-5v85: The crystal structure of the protein of DegV family COG1307 from ... -

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Basic information

Entry
Database: PDB / ID: 5v85
TitleThe crystal structure of the protein of DegV family COG1307 from Ruminococcus gnavus ATCC 29149 (alternative refinement of PDB 3JR7 with Vaccenic acid)
ComponentsEDD domain protein, DegV family
KeywordsTRANSPORT PROTEIN / DEGV / GUT MICROBIOME / STRUCTURAL GENOMICS / PSI-2 / C18:1 / Vaccenic acid
Function / homology
Function and homology information


DegV, N-terminal domain, peripheral subdomain / Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Dihydroxyacetone kinase; domain 1 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / Rubrerythrin, domain 2 / Single Sheet ...DegV, N-terminal domain, peripheral subdomain / Hypothetical Protein Tm841; Chain: A;domain 3 - #10 / Dihydroxyacetone kinase; domain 1 / DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / Hypothetical Protein Tm841; Chain: A;domain 3 / Rubrerythrin, domain 2 / Single Sheet / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / VACCENIC ACID / EDD domain protein, DegV family
Similarity search - Component
Biological speciesRuminococcus gnavus ATCC 29149 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.003 Å
AuthorsCuypers, M.G. / Ericson, M. / subramanian, C. / White, S.W. / Rock, C.O.
CitationJournal: to be published
Title: The crystal structure of the protein of DegV family COG1307 with unknown function from Ruminococcus gnavus ATCC 29149
Authors: Zhang, R. / Hatzos, C. / Clancy, S. / Joachimiak, A.
History
DepositionMar 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Remark 0This entry reflects an alternative modeling of the original data in 3JR7, determined by R.ZHANG,C. ...This entry reflects an alternative modeling of the original data in 3JR7, determined by R.ZHANG,C.HATZOS,S.CLANCY,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG)
Remark 200SEE THE ORIGINAL DATA, ENTRY 3JR7
Remark 280SEE THE ORIGINAL DATA, ENTRY 3JR7

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EDD domain protein, DegV family
B: EDD domain protein, DegV family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,25910
Polymers67,2682
Non-polymers9918
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-34 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.899, 96.899, 159.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein EDD domain protein, DegV family


Mass: 33634.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus ATCC 29149 (bacteria)
Gene: RUMGNA_03254 / Plasmid: PMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A7B6P0
#2: Chemical ChemComp-VCA / VACCENIC ACID / (11E)-OCTADEC-11-ENOIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 289 K / Details: THIS IS UNALTERED ORIGINAL DATA FROM ENTRY 3JR7 / Method: vapor diffusion, sitting drop
Details: 0.2M SODIUM CHLORIDE, 0.1M PHOSPHATE-CITRATE, 10%PEG3000, PH 4.2

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Data collection

DiffractionMean temperature: 100 K / Details: THIS IS UNALTERED ORIGINAL DATA FROM ENTRY 3JR7
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Details: THIS IS UNALTERED ORIGINAL DATA FROM ENTRY 3JR7 / Wavelength: 0.97915 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 4, 2008 / Details: THIS IS UNALTERED ORIGINAL DATA FROM ENTRY 3JR7
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→83.92 Å / Num. obs: 58785 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Details: THIS IS UNALTERED ORIGINAL DATA FROM ENTRY 3JR7 / Net I/σ(I): 17.85

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.003→29.887 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.2
RfactorNum. reflection% reflection
Rfree0.1977 2970 5.05 %
Rwork0.1685 --
obs0.1699 58785 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.003→29.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4287 0 62 609 4958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034503
X-RAY DIFFRACTIONf_angle_d0.5336068
X-RAY DIFFRACTIONf_dihedral_angle_d6.4233771
X-RAY DIFFRACTIONf_chiral_restr0.044686
X-RAY DIFFRACTIONf_plane_restr0.003784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0028-2.03560.27821350.2282637X-RAY DIFFRACTION99
2.0356-2.07070.23721390.19612640X-RAY DIFFRACTION100
2.0707-2.10840.21071370.18542644X-RAY DIFFRACTION100
2.1084-2.14890.21071290.17562657X-RAY DIFFRACTION100
2.1489-2.19280.2241530.18312624X-RAY DIFFRACTION100
2.1928-2.24040.20841280.17852623X-RAY DIFFRACTION100
2.2404-2.29250.24011520.17852634X-RAY DIFFRACTION100
2.2925-2.34980.24071400.17892642X-RAY DIFFRACTION100
2.3498-2.41330.18891400.17582655X-RAY DIFFRACTION100
2.4133-2.48430.19261350.17252661X-RAY DIFFRACTION100
2.4843-2.56450.20971380.17582640X-RAY DIFFRACTION100
2.5645-2.65610.21181480.17752642X-RAY DIFFRACTION100
2.6561-2.76230.2261600.18122649X-RAY DIFFRACTION100
2.7623-2.8880.2261230.19052677X-RAY DIFFRACTION100
2.888-3.04010.21751420.17472661X-RAY DIFFRACTION100
3.0401-3.23030.19171670.18142642X-RAY DIFFRACTION99
3.2303-3.47940.20251580.15952633X-RAY DIFFRACTION99
3.4794-3.82890.19251360.14742681X-RAY DIFFRACTION99
3.8289-4.38150.15391410.13532671X-RAY DIFFRACTION99
4.3815-5.51450.15571420.14052704X-RAY DIFFRACTION98
5.5145-29.89030.18631270.18842798X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 22.3722 Å / Origin y: 41.8283 Å / Origin z: 40.4923 Å
111213212223313233
T0.1071 Å20.0001 Å2-0.0089 Å2-0.1365 Å2-0.0038 Å2--0.1569 Å2
L0.3545 °2-0.1156 °2-0.0071 °2-0.2636 °2-0.0763 °2--0.543 °2
S0.0304 Å °0.0349 Å °0.0067 Å °-0.0393 Å °-0.0046 Å °0.0215 Å °0.0074 Å °-0.0202 Å °0.0003 Å °
Refinement TLS groupSelection details: all

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