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- PDB-3ufi: Crystal structure of a putative cell adhesion protein (BACOVA_049... -

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Basic information

Entry
Database: PDB / ID: 3ufi
TitleCrystal structure of a putative cell adhesion protein (BACOVA_04980) from Bacteroides ovatus ATCC 8483 at 2.18 A resolution
Componentshypothetical protein BACOVA_04980
KeywordsCELL ADHESION / FIMBRIAL PROTEIN / Major fimbrial subunit protein (FimA) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyImmunoglobulin-like - #2630 / Fimbrillin-like / Fimbrillin-like 1, N-terminal / Fimbrillin-like 1 / Fimbrillin-like / Immunoglobulin-like / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.18 Å
AuthorsJoint Center for Structural Genomics (JCSG)
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
DepositionNov 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Apr 22, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein BACOVA_04980
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8049
Polymers33,2781
Non-polymers5268
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)176.660, 176.660, 51.171
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein hypothetical protein BACOVA_04980


Mass: 33277.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_04980 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7M4D9
#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.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT (RESIDUES 25-320) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...1. THE CONSTRUCT (RESIDUES 25-320) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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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: 6.93 Å3/Da / Density % sol: 82.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.4M ammonium sulfate, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.18→44.278 Å / Num. obs: 48085 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.74 % / Biso Wilson estimate: 37.962 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 11.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.18-2.267.711.082.137419485499.7
2.26-2.350.9662.237245474499.9
2.35-2.450.6123.3353844489100
2.45-2.580.5054379564819100
2.58-2.750.3226.1392725030100
2.75-2.960.2198.8373084737100
2.96-3.250.13213.3366964678100
3.25-3.720.08119.8371864836100
3.72-4.680.0625.5369594871100
4.68-44.280.06427.136835502799.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.18→44.278 Å / Cor.coef. Fo:Fc: 0.9378 / Cor.coef. Fo:Fc free: 0.9261 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. SULFATE AND CHLORIDE IONS MODELLED ARE PRESENT IN CRYSTALLIZATION/CRYO/PURIFICATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 2433 5.06 %RANDOM
Rwork0.1776 ---
obs0.1788 48065 99.96 %-
Displacement parametersBiso max: 128.94 Å2 / Biso mean: 42.8367 Å2 / Biso min: 11.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.1002 Å20 Å20 Å2
2---3.1002 Å20 Å2
3---6.2004 Å2
Refine analyzeLuzzati coordinate error obs: 0.251 Å
Refinement stepCycle: LAST / Resolution: 2.18→44.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 24 328 2512
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d996SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes330HARMONIC5
X-RAY DIFFRACTIONt_it2273HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion311SEMIHARMONIC5
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_contact2630SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2273HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3112HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion4.25
X-RAY DIFFRACTIONt_other_torsion2.55
LS refinement shellResolution: 2.18→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2334 178 5.01 %
Rwork0.2352 3374 -
all0.2351 3552 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: 57.3782 Å / Origin y: 69.1055 Å / Origin z: 35.7317 Å
111213212223313233
T-0.0209 Å20.072 Å2-0.002 Å2-0.0066 Å20.0146 Å2---0.0842 Å2
L1.5623 °2-0.9818 °20.1533 °2-1.524 °2-0.0126 °2--0.3856 °2
S0.0096 Å °0.0168 Å °0.0323 Å °0.0165 Å °-0.0327 Å °-0.1286 Å °-0.0902 Å °-0.1224 Å °0.0231 Å °
Refinement TLS groupSelection details: { A|33 - A|310 }

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