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- PDB-5cag: Crystal structure of a putative adhesin (BACOVA_02677) from Bacte... -

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Basic information

Entry
Database: PDB / ID: 5cag
TitleCrystal structure of a putative adhesin (BACOVA_02677) from Bacteroides ovatus ATCC 8483 at 3.00 A resolution (PSI Community Target, Nakayama)
ComponentsUncharacterized protein
KeywordsCELL ADHESION / adhesin / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF5119 / Domain of unknown function (DUF5119) / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Putative fimbrium anchoring subunit Fim4B
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Nakayama, K.
CitationJournal: Cell / Year: 2016
Title: A Distinct Type of Pilus from the Human Microbiome.
Authors: Xu, Q. / Shoji, M. / Shibata, S. / Naito, M. / Sato, K. / Elsliger, M.A. / Grant, J.C. / Axelrod, H.L. / Chiu, H.J. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Deacon, A.M. / Godzik, A. / ...Authors: Xu, Q. / Shoji, M. / Shibata, S. / Naito, M. / Sato, K. / Elsliger, M.A. / Grant, J.C. / Axelrod, H.L. / Chiu, H.J. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Curtis, M.A. / Nakayama, K. / Wilson, I.A.
History
DepositionJun 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,14510
Polymers35,2811
Non-polymers8659
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,29020
Polymers70,5612
Non-polymers1,72918
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area5970 Å2
ΔGint-256 kcal/mol
Surface area31010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.391, 98.391, 217.037
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Uncharacterized protein


Mass: 35280.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153 / Gene: BACOVA_02677 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7LXW1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
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: 4.3 Å3/Da / Density % sol: 71.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.2000M lithium sulfate, 2.0000M ammonium sulfate, 0.1M CAPS pH 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9116,0.9794,0.9792
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2014
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91161
20.97941
30.97921
ReflectionResolution: 3→49.195 Å / Num. obs: 13098 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.491 % / Biso Wilson estimate: 81.271 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.098 / Net I/σ(I): 18.18 / Num. measured all: 125002
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
3-3.110.8321.3781.612696130313031.4561100
3.11-3.220.9020.982.211494113811381.033100
3.22-3.350.9670.5423.911514115311530.571100
3.35-3.50.9910.3515.911127114011380.37199.8
3.5-3.680.9960.2288.510479113111300.24199.9
3.68-3.910.9950.1651211078116611660.175100
3.91-4.210.9980.1117.311501116411640.117100
4.21-4.630.9990.06926.111442118711850.07299.8
4.63-5.290.9990.05132.910886119511940.05499.9
5.29-6.630.9990.05534.311474122212200.05899.8
6.6310.03349.211311139113790.03599.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XDSdata reduction
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
SHELXDphasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: MAD / Resolution: 3→49.195 Å / Cor.coef. Fo:Fc: 0.9216 / Cor.coef. Fo:Fc free: 0.9328 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 4. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 5. THE SEQUENCE IS NUMBERED ACCORDING PATRIC DB ENTRY VBIBacOva42630_2252 WHICH CONTAINS ADDITIONAL N-TERM SIGNAL SEQUENCE (NOT PRESENT IN UNIPROT ENTRY VBIBacOva42630_2252).
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 621 4.74 %RANDOM
Rwork0.185 ---
obs0.1861 13097 99.73 %-
Displacement parametersBiso max: 225.89 Å2 / Biso mean: 107.9401 Å2 / Biso min: 59.6 Å2
Baniso -1Baniso -2Baniso -3
1--17.1923 Å20 Å20 Å2
2---17.1923 Å20 Å2
3---34.3845 Å2
Refine analyzeLuzzati coordinate error obs: 0.564 Å
Refinement stepCycle: LAST / Resolution: 3→49.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 45 0 2239
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1044SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes314HARMONIC5
X-RAY DIFFRACTIONt_it2273HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion301SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2361SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2273HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3085HARMONIC21.27
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion3.19
LS refinement shellResolution: 3→3.24 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3201 124 4.76 %
Rwork0.2573 2479 -
all0.2602 2603 -
obs--99.73 %
Refinement TLS params.Method: refined / Origin x: 25.9473 Å / Origin y: 60.0926 Å / Origin z: 117.583 Å
111213212223313233
T-0.2934 Å2-0.0364 Å20.1122 Å2--0.0645 Å20.1096 Å2---0.2589 Å2
L1.6208 °2-0.9087 °20.1316 °2-5.8348 °2-1.0216 °2--2.1467 °2
S0.0861 Å °-0.0604 Å °-0.1079 Å °0.1382 Å °-0.4737 Å °-0.3356 Å °-0.0746 Å °0.4254 Å °0.3876 Å °
Refinement TLS groupSelection details: {A|0 - 306}

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