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- PDB-2rb6: X-Ray structure of the protein Q8EI81. Northeast Structural Genom... -

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Basic information

Entry
Database: PDB / ID: 2rb6
TitleX-Ray structure of the protein Q8EI81. Northeast Structural Genomics Consortium target SoR78A
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / Q8EI81_SHEON / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Protein of unknown function DUF903 / : / Bacterial protein of unknown function (DUF903) / SH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Mainly Beta
Similarity search - Domain/homology
Lipoprotein YgdI/YgdR-like SH3-like domain-containing protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, H. / Mao, L. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, H. / Mao, L. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-Ray structure of the protein Q8EI81.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, H. / Mao, L. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionSep 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)15,0252
Polymers15,0252
Non-polymers00
Water82946
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)7,5131
Polymers7,5131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)7,5131
Polymers7,5131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Uncharacterized protein

B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)15,0252
Polymers15,0252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.880, 109.354, 27.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uncharacterized protein


Mass: 7512.694 Da / Num. of mol.: 2 / Fragment: Residues 25-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_0963 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EI81
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.93 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 6
Details: 0.1M NaNO3, 0.1M MES, 20% PEG 4000, pH 6.0, MICROBATCH UNDER OIL, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 14617 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 50.5 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 19.7
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 5.3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.92 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 129958.77 / 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 in phasing. Bulk solvent model was used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.28 443 4.9 %RANDOM
Rwork0.241 ---
obs0.241 9058 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.8393 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---4.07 Å20 Å2
3---3.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms926 0 0 46 972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.58
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.457 58 4.2 %
Rwork0.37 1312 -
obs--84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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