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- PDB-5uc0: Crystal Structure of Beta-barrel-like, Uncharacterized Protein of... -

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Basic information

Entry
Database: PDB / ID: 5uc0
TitleCrystal Structure of Beta-barrel-like, Uncharacterized Protein of COG5400 from Brucella abortus
ComponentsUncharacterized Protein COG5400
KeywordsHYDROLASE / beta barrel-like / beta-structure / Chicago Center for Functional Annotation / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homologyEipA-like / Envelope integrity protein A / Uncharacterized protein
Function and homology information
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.73 Å
AuthorsKim, Y. / Bigelow, L. / Endres, M. / Babnigg, G. / Crosson, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Mol. Microbiol. / Year: 2018
Title: Periplasmic protein EipA determines envelope stress resistance and virulence in Brucella abortus.
Authors: Herrou, J. / Willett, J.W. / Fiebig, A. / Varesio, L.M. / Czyz, D.M. / Cheng, J.X. / Ultee, E. / Briegel, A. / Bigelow, L. / Babnigg, G. / Kim, Y. / Crosson, S.
History
DepositionDec 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Derived calculations / Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.5Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.6Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized Protein COG5400
B: Uncharacterized Protein COG5400
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,70610
Polymers34,7742
Non-polymers9328
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-55 kcal/mol
Surface area14280 Å2
2
A: Uncharacterized Protein COG5400
B: Uncharacterized Protein COG5400
hetero molecules

A: Uncharacterized Protein COG5400
B: Uncharacterized Protein COG5400
hetero molecules

A: Uncharacterized Protein COG5400
B: Uncharacterized Protein COG5400
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,11830
Polymers104,3236
Non-polymers2,79524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area15150 Å2
ΔGint-288 kcal/mol
Surface area35560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.075, 113.075, 64.308
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-457-

HOH

21A-463-

HOH

Detailsbiological assemblies are dimer and hexamer by size exclusion chromatography

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Components

#1: Protein Uncharacterized Protein COG5400


Mass: 17387.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (strain 2308) (bacteria)
Strain: 2308 / Gene: BAB1_1612 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 gold / References: UniProt: Q2YQA6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5, 30 %(w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 49076 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 23.12 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 24.9
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.799 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2411: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.73→32.642 Å / Cross valid method: THROUGHOUT / Phase error: 23.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 2539 5.17 %random
Rwork0.1763 ---
obs0.179 49069 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→32.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 54 322 2774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072531
X-RAY DIFFRACTIONf_angle_d0.8763422
X-RAY DIFFRACTIONf_dihedral_angle_d17.629878
X-RAY DIFFRACTIONf_chiral_restr0.053354
X-RAY DIFFRACTIONf_plane_restr0.005441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7276-1.76080.2721390.25372562X-RAY DIFFRACTION94
1.7608-1.79680.2621260.25252561X-RAY DIFFRACTION95
1.7968-1.83580.20421370.24942578X-RAY DIFFRACTION95
1.8358-1.87850.30231620.24032548X-RAY DIFFRACTION94
1.8785-1.92550.21891300.24952583X-RAY DIFFRACTION95
1.9255-1.97750.24541170.23482580X-RAY DIFFRACTION95
1.9775-2.03570.23891580.23182570X-RAY DIFFRACTION94
2.0357-2.10140.26271250.24642567X-RAY DIFFRACTION95
2.1014-2.17650.25091400.23152583X-RAY DIFFRACTION95
2.1765-2.26360.23611560.22332567X-RAY DIFFRACTION94
2.2636-2.36650.23731170.22422614X-RAY DIFFRACTION96
2.3665-2.49120.25731310.21842592X-RAY DIFFRACTION95
2.4912-2.64710.2951330.20792618X-RAY DIFFRACTION95
2.6471-2.85130.20311500.19932567X-RAY DIFFRACTION94
2.8513-3.13780.26331410.18052593X-RAY DIFFRACTION95
3.1378-3.59080.18871760.14322572X-RAY DIFFRACTION94
3.5908-4.52010.17251450.10542625X-RAY DIFFRACTION95
4.5201-25.88170.14671560.12822630X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.88840.6517-0.16871.46520.3720.66370.031-0.02660.0407-0.0214-0.10380.22930.0955-0.06980.16580.2476-0.007-0.05130.177-0.08550.030942.199511.620539.6061
22.65061.73012.53582.18881.36092.97830.01170.0397-0.22990.33950.1634-0.27890.62350.5908-0.12940.36490.1336-0.01840.4629-0.07780.145755.179419.355347.7941
31.40.0337-0.46231.1121-0.00653.00970.00790.1763-0.0127-0.16870.00430.107-0.0524-0.01990.0720.23740.0131-0.05950.1632-0.04520.025939.924919.122937.6274
40.5975-0.3036-0.16050.86970.35950.1512-0.0142-0.11020.0320.023-0.0232-0.0247-0.1524-0.14140.02650.2772-0.02030.00670.2316-0.0160.044449.940723.279639.4074
56.48212.1582-1.10273.1356-0.57453.4343-0.0670.3394-0.3809-0.2312-0.03770.3289-0.0491-0.40990.09150.15650.090.03670.2555-0.01460.168223.066430.58164.6637
62.81520.84520.15233.26080.76872.3865-0.16090.0971-0.4132-0.2305-0.06920.10680.1955-0.25410.20670.18620.00480.05850.22970.0110.108329.092425.105664.7099
74.24051.46621.83352.50690.1660.9019-0.27380.70370.0221-0.36980.1497-0.21-0.30860.07780.13620.2597-0.0376-0.00010.2495-0.04610.074543.461537.728567.9858
80.7559-0.0380.47391.01130.76621.1633-0.0808-0.26870.00970.28190.03340.12370.0138-0.11740.06920.25250.03280.04120.2784-0.0180.056634.30433.975975.8077
90.00220.0004-0.00360.0251-0.02140.02270.60951.36060.7612-1.4677-0.3206-0.0771-0.4119-0.2982-0.29180.9626-0.11780.11050.7480.21290.577644.659739.199958.5861
100.6830.18980.29130.79170.34360.6905-0.0161-0.0948-0.04620.116300.04980.01180.00870.00670.22750.05250.0690.26240.0214-0.013139.157427.120768.9103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 114 )
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 124 )
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 174 )
4X-RAY DIFFRACTION4chain 'A' and (resid 175 through 198 )
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 58 )
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 84 )
7X-RAY DIFFRACTION7chain 'B' and (resid 85 through 100 )
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 114 )
9X-RAY DIFFRACTION9chain 'B' and (resid 115 through 124 )
10X-RAY DIFFRACTION10chain 'B' and (resid 125 through 198 )

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