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- PDB-2ra8: Crystal structure of the Q64V53_BACFR protein from Bacteroides fr... -

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Basic information

Entry
Database: PDB / ID: 2ra8
TitleCrystal structure of the Q64V53_BACFR protein from Bacteroides fragilis. Northeast Structural Genomics Consortium target BfR43
ComponentsUncharacterized protein Q64V53_BACFR
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Q64V53 / WGR DOMAIN / LRR DOMAIN / LEUCINE RICH REPEATS / BFR43 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


WGR domain / : / : / q64v53_bacfr protein fold / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) ...WGR domain / : / : / q64v53_bacfr protein fold / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Single Sheet / Leucine-rich repeat domain superfamily / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
WGR domain-containing protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsVorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Wang, D. / Cunningham, K. / Maglaqui, M. / Owens, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Wang, D. / Cunningham, K. / Maglaqui, M. / Owens, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Q64V53_BACFR protein from Bacteroides fragilis.
Authors: Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Wang, D. / Cunningham, K. / Maglaqui, M. / Owens, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionSep 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Q64V53_BACFR


Theoretical massNumber of molelcules
Total (without water)41,8531
Polymers41,8531
Non-polymers00
Water4,143230
1
A: Uncharacterized protein Q64V53_BACFR

A: Uncharacterized protein Q64V53_BACFR


Theoretical massNumber of molelcules
Total (without water)83,7052
Polymers83,7052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.261, 65.237, 60.008
Angle α, β, γ (deg.)90.00, 111.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

DetailsDimer according to the aggregation analysis; second part of the biological assembly is generated by -x+1,y,-z+1 symmetry operator.

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Components

#1: Protein Uncharacterized protein Q64V53_BACFR


Mass: 41852.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: YCH46 / Gene: BF1877 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q64V53
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16-18% PEG 3350, 0.2M Magnesium acetate, 0.1M Cacodylic acid pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 52396 / Num. obs: 52396 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 9.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.35
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 2.25 / Num. unique all: 5541 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→19.39 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 622181.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: 1. The Friedel pairs were used for phasing. 2. Cys 116 was modified to s-(dimethylarsenic)cysteine by cacodylic buffer. 3. Tyr 316 is located in a generously allowed position on Ramachandran ...Details: 1. The Friedel pairs were used for phasing. 2. Cys 116 was modified to s-(dimethylarsenic)cysteine by cacodylic buffer. 3. Tyr 316 is located in a generously allowed position on Ramachandran plot. However, Tyr 316 electron density is very well defined and could be interpreted unambiguously.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1730 3.9 %RANDOM
Rwork0.225 ---
obs0.225 44385 79.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.8472 Å2 / ksol: 0.348442 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.35 Å20 Å21.57 Å2
2---1.64 Å20 Å2
3---5.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 0 230 3003
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
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: 1.95→2.07 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 197 3.6 %
Rwork0.259 5339 -
obs--59.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4cas_mod1.parcas_mod1.top

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