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- PDB-2o3i: X-ray Crystal Structure of Protein CV_3147 from Chromobacterium v... -

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Basic information

Entry
Database: PDB / ID: 2o3i
TitleX-ray Crystal Structure of Protein CV_3147 from Chromobacterium violaceum. Northeast Structural Genomics Consortium Target CvR68.
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / CvR68 / Q7NTB2 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


CV3147-like / CV3147-like / CV3147-like fold / CV3147-like domain / Protein of unknown function DUF917 / Protein of unknown function DUF917, C-terminal / Protein of unknown function DUF917, N-terminal / : / Protein of unknown function (DUF917), N-terminal / Protein of unknown function DUF917, C-terminal ...CV3147-like / CV3147-like / CV3147-like fold / CV3147-like domain / Protein of unknown function DUF917 / Protein of unknown function DUF917, C-terminal / Protein of unknown function DUF917, N-terminal / : / Protein of unknown function (DUF917), N-terminal / Protein of unknown function DUF917, C-terminal / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DUF917 domain-containing protein
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsVorobiev, S.M. / Chen, Y. / Seetharaman, J. / Cunningham, K. / Ma, L.C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. ...Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Cunningham, K. / Ma, L.C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the hypothetical protein Q7NTB2_CHRVO from Chromobacterium violaceum
Authors: Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Cunningham, K. / Ma, L.C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionDec 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT IS BASED ON LIGHT SCATTERING AND GEL FILTRATION DATA, AND THAT OTHER POSSIBLE MULTIMERIZATION STATE IS PURELY CRYSTALLOGRAPHIC.
Remark 999 SEQUENCE AUTHORS STATE THAT THE MUTATIONS SER271PRO AND GLY395ARG ARE THE RESULT OF CLONING PROCEDURE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)86,5652
Polymers86,5652
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-12 kcal/mol
Surface area28280 Å2
MethodPISA
2
A: Hypothetical protein
B: Hypothetical protein

A: Hypothetical protein
B: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)173,1304
Polymers173,1304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area5890 Å2
ΔGint-42 kcal/mol
Surface area54020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.336, 125.608, 65.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsDimer (according to Gel-filtration)

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Components

#1: Protein Hypothetical protein


Mass: 43282.414 Da / Num. of mol.: 2 / Mutation: S271P, G395R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: HAMAP536 / Gene: CV_3147 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7NTB2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.77 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 9
Details: 40% PEG 1000, 0.1 M Magnesium sulfate, 0.1 M TAPS, pH 9.0, Microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 65131 / Num. obs: 65131 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 4.9 / Num. unique all: 6566 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 81883.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used for phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2218 3.9 %RANDOM
Rwork0.198 ---
obs0.198 57387 87.9 %-
all-65131 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.1937 Å2 / ksol: 0.316507 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--15.18 Å20 Å2
3----14.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5386 0 0 227 5613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 337 4 %
Rwork0.222 8091 -
obs--77.6 %
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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