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- PDB-3pay: Crystal structure of a putative adhesin (BACOVA_04077) from Bacte... -

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Basic information

Entry
Database: PDB / ID: 3pay
TitleCrystal structure of a putative adhesin (BACOVA_04077) from Bacteroides ovatus at 2.50 A resolution
Componentsputative adhesin
KeywordsCELL ADHESION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Immunoglobulin-like - #2090 / Immunoglobulin-like - #2100 / Fimbrium subunit FimB/Mfa2/Mfa3 / Fimbrillin-A associated anchor proteins Mfa1 and Mfa2 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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
DepositionOct 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Apr 22, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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: putative adhesin
B: putative adhesin
C: putative adhesin
D: putative adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6567
Polymers144,3374
Non-polymers3183
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9570 Å2
ΔGint-20 kcal/mol
Surface area50690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.107, 78.776, 84.105
Angle α, β, γ (deg.)93.880, 102.080, 103.540
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
putative adhesin


Mass: 36084.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_04077 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7M1U3
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 20-332) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THIS CONSTRUCT (RESIDUES 20-332) 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.

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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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2000M calcium acetate, 10.0000% polyethylene glycol 8000, 0.1M Imidazole pH 8.0, 0.003 M S-adenosyl methionine (SAM), 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: 0.9537,0.9796,0.9793
DetectorType: ADSC Q315 / Detector: CCD / Date: Sep 16, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97961
30.97931
ReflectionResolution: 2.5→29.465 Å / Num. obs: 54374 / % possible obs: 88.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 50.744 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 6.24
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.5-2.590.351294298670175.8
2.59-2.690.2912.3103819575187.7
2.69-2.810.2162.8106839875188.2
2.81-2.960.1683.51088610125189.1
2.96-3.150.1174.71110210351189.1
3.15-3.390.0796.41068510029189.7
3.39-3.730.0648.11080110197190.3
3.73-4.260.0519.71066610126190.5
4.26-5.350.04410.71063010203190.4
5.35-29.4650.047111110610781193.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.465 Å / Cor.coef. Fo:Fc: 0.9025 / Cor.coef. Fo:Fc free: 0.8861 / 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. ACETATE (ACT) AND POLYETHYLENE GLYCOL (PEG) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED INTO THE STRUCTURE. 3. THE AUTONCS COMMAND OPTION OF BUSTER WAS IMPLEMENTED DURING REFINEMENT FOR APPLICATION OF NCS RESTRAINTS. 4. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 2758 5.07 %RANDOM
Rwork0.2138 ---
obs0.2151 54348 --
Displacement parametersBiso max: 121.15 Å2 / Biso mean: 42.6014 Å2 / Biso min: 9.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.2442 Å2-2.4254 Å26.4394 Å2
2--0.0085 Å2-5.6578 Å2
3---1.2357 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9732 0 21 239 9992
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4470SINUSOIDAL10
X-RAY DIFFRACTIONt_trig_c_planes269HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1453HARMONIC5
X-RAY DIFFRACTIONt_it10023HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1267SEMIHARMONIC5
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_contact11126SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10023HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13657HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion1.96
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2959 181 4.98 %
Rwork0.2133 3454 -
all0.2175 3635 -
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)
10.9147-1.10920.70552.5016-1.40612.16580.1660.32270.0477-0.3909-0.3506-0.21730.1690.48790.1846-0.04870.1037-0.0986-0.0164-0.0799-0.266934.2159-8.06632.9792
20.64780.08990.6511.7412-0.83511.9506-0.04840.02540.05730.2141-0.0111-0.228-0.07930.07820.0594-0.0920.0244-0.1299-0.0905-0.1283-0.127348.6743-15.364776.758
30.7977-0.50090.35881.5043-0.57451.93370.01390.0033-0.0331-0.0593-0.03850.0951-0.0545-0.10240.0246-0.04490.0176-0.0915-0.1667-0.1355-0.09948.69012.32354.2824
40.9312-0.430.59511.8462-0.4961.3350.0661-0.0779-0.13990.1185-0.03920.17180.1021-0.0766-0.0269-0.02070.0119-0.065-0.199-0.1316-0.10822.9665-38.474970.5274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 331
2X-RAY DIFFRACTION2{ B|* }B0 - 331
3X-RAY DIFFRACTION3{ C|* }C20 - 331
4X-RAY DIFFRACTION4{ D|* }D0 - 331

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