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- PDB-2qti: Crystal structure of the UPF0352 protein SO_2176 from Shewanella ... -

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Basic information

Entry
Database: PDB / ID: 2qti
TitleCrystal structure of the UPF0352 protein SO_2176 from Shewanella oneidensis. NESG target SoR77.
ComponentsUPF0352 protein SO_2176
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Y2176_SHEON / UPF0352 / SO_2176 / PF07208 / NESG / SoR77 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyUncharacterised protein family UPF0352 / YejL-like superfamily / Protein of unknown function (DUF1414) / YejL-like / YejL-like / Orthogonal Bundle / Mainly Alpha / UPF0352 protein SO_2176
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsVorobiev, S.M. / Su, M. / Seetharaman, J. / Kuzin, A.P. / Wang, D. / Cunningham, K. / Owens, L. / Maglaqui, M. / Fang, Y. / Xiao, R. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Kuzin, A.P. / Wang, D. / Cunningham, K. / Owens, L. / Maglaqui, M. / Fang, Y. / 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 UPF0352 protein SO_2176 from Shewanella oneidensis.
Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Kuzin, A.P. / Wang, D. / Cunningham, K. / Owens, L. / Maglaqui, M. / Fang, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionAug 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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

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Assembly

Deposited unit
A: UPF0352 protein SO_2176


Theoretical massNumber of molelcules
Total (without water)9,0401
Polymers9,0401
Non-polymers00
Water34219
1
A: UPF0352 protein SO_2176

A: UPF0352 protein SO_2176


Theoretical massNumber of molelcules
Total (without water)18,0802
Polymers18,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.576, 50.576, 62.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsDimer by gel filtration. The second part of the biological assembly is generated by y, x, -z+1 symmetry operator.

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Components

#1: Protein UPF0352 protein SO_2176


Mass: 9040.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_2176 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8EF26
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 4
Details: 40% PEG 1000, 0.1M Ammonium phosphate, 0.1M Sodium citrate pH 4.0, MICROBATCH UNDER OIL, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97913 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 7182 / Num. obs: 7182 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 41.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 4.47 / Num. unique all: 721 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→39.32 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 74338.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used for phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.232 615 9.8 %RANDOM
Rwork0.223 ---
obs0.223 6260 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.1581 Å2 / ksol: 0.397721 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2---1.28 Å20 Å2
3---2.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms498 0 0 19 517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
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: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.206 93 10.7 %
Rwork0.211 774 -
obs--76.4 %
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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