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- PDB-3up6: Crystal structure of a putative cell adhesion protein (BACOVA_040... -

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Basic information

Entry
Database: PDB / ID: 3up6
TitleCrystal structure of a putative cell adhesion protein (BACOVA_04078) from Bacteroides ovatus ATCC 8483 at 2.80 A resolution
Componentshypothetical protein BACOVA_04078
KeywordsCELL ADHESION / Major fimbrial subunit protein (FimA) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyImmunoglobulin-like - #3380 / Immunoglobulin-like - #2580 / Major fimbrial subunit protein, N-terminal / Major fimbrial subunit protein (FimA) / pilus / Immunoglobulin-like / Sandwich / Mainly Beta / P_gingi_FimA domain-containing protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 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 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: hypothetical protein BACOVA_04078
B: hypothetical protein BACOVA_04078


Theoretical massNumber of molelcules
Total (without water)75,8502
Polymers75,8502
Non-polymers00
Water2,234124
1
A: hypothetical protein BACOVA_04078


Theoretical massNumber of molelcules
Total (without water)37,9251
Polymers37,9251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: hypothetical protein BACOVA_04078


Theoretical massNumber of molelcules
Total (without water)37,9251
Polymers37,9251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.043, 91.138, 106.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein BACOVA_04078


Mass: 37924.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_04078 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7M1U4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 25-370) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 25-370) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.33
Details: 1.0M lithium chloride, 18.0% polyethylene glycol 6000, 0.1M sodium citrate - citric acid pH 5.33, Additive: 0.001 M iron (II) chloride, 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: 0.9793,0.9537
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.95371
ReflectionResolution: 2.8→45.931 Å / Num. obs: 18914 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4.67 % / Biso Wilson estimate: 58.693 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 9.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.8-2.94.880.7192.089099186599.9
2.9-3.020.5412.89474196099.9
3.02-3.150.3893.88675179599.8
3.15-3.320.2865.19356194399.6
3.32-3.520.2446.47713172794.6
3.52-3.790.1588.98418187997.8
3.79-4.170.128118042182694.9
4.17-4.770.07815.98803191698.5
4.77-5.980.07815.69217193998.7
5.98-45.930.06618.39503206496.9

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Phasing

PhasingMethod: MAD

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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
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→45.931 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.8658 / Occupancy max: 1 / Occupancy min: 0.75 / 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. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 973 5.13 %RANDOM
Rwork0.2026 ---
obs0.2051 18950 98.38 %-
Displacement parametersBiso max: 124.58 Å2 / Biso mean: 44.0511 Å2 / Biso min: 7.82 Å2
Baniso -1Baniso -2Baniso -3
1--5.9308 Å20 Å20 Å2
2---11.5368 Å20 Å2
3---17.4676 Å2
Refine analyzeLuzzati coordinate error obs: 0.367 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4854 0 0 124 4978
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2291SINUSOIDAL8
X-RAY DIFFRACTIONt_trig_c_planes130HARMONIC2
X-RAY DIFFRACTIONt_gen_planes714HARMONIC5
X-RAY DIFFRACTIONt_it4921HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion714SEMIHARMONIC5
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_contact5418SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4921HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6698HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion2.08
LS refinement shellResolution: 2.8→2.95 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3136 132 4.83 %
Rwork0.2244 2599 -
all0.229 2731 -
obs--98.38 %
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)
10.93220.3437-1.15880.9814-0.87383.8456-0.03950.0578-0.0007-0.0577-0.03560.01590.1127-0.18020.0751-0.1403-0.0057-0.0504-0.21530.01220.006755.993136.433689.6994
21.5930.8294-1.77571.0192-1.28834.0917-0.08010.00460.0161-0.1567-0.0022-0.06250.17830.03430.0824-0.15230.0046-0.0433-0.2420.03110.010518.201636.716584.4286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|35 - 358 }A35 - 358
2X-RAY DIFFRACTION2{ B|35 - 358 }B35 - 358

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