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- PDB-4eps: Crystal structure of a fimbrial protein (BACOVA_04982) from Bacte... -

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Basic information

Entry
Database: PDB / ID: 4eps
TitleCrystal structure of a fimbrial protein (BACOVA_04982) from Bacteroides ovatus ATCC 8483 at 1.85 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / HYPOTHETICAL PROTEIN (DUF3988) / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


pilus / cell outer membrane
Similarity search - Function
Immunoglobulin-like - #3570 / Fimbrillin-like / Fimbrillin-like 1, N-terminal / Fimbrillin-like 1 / Fimbrillin-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative fimbrium tip subunit Fim1C
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 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
Revision 1.6Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,97630
Polymers57,5201
Non-polymers2,45629
Water11,818656
1
A: hypothetical protein
hetero molecules

A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,95160
Polymers115,0392
Non-polymers4,91258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area13190 Å2
ΔGint-164 kcal/mol
Surface area45030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.956, 77.956, 250.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein hypothetical protein


Mass: 57519.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_04982 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7M4E1
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 26-534) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 26-534) 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: 3.31 Å3/Da / Density % sol: 62.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.6M ammonium sulfate, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.85→29.056 Å / Num. all: 67064 / Num. obs: 67064 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rsym value: 0.114 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.98.60.9932.44200848600.993100
1.9-1.958.50.7513.14050747540.751100
1.95-2.017.70.5313.83582746310.531100
2.01-2.078.80.424.93917944760.42100
2.07-2.149.20.34864028143570.348100
2.14-2.219.20.27873890242460.278100
2.21-2.298.70.22883583041150.228100
2.29-2.398.40.1938.73264538970.19399.9
2.39-2.4980.1619.83035237850.16199.9
2.49-2.629.30.14711.73369736280.147100
2.62-2.769.10.13113.13167434750.131100
2.76-2.9390.11514.42937132690.115100
2.93-3.138.20.099162545830970.09999.9
3.13-3.388.90.09118.62586829100.091100
3.38-3.79.40.08720.72520726940.087100
3.7-4.149.10.08121.42230924420.081100
4.14-4.787.60.07720.11640021680.07799.7
4.78-5.859.20.08421.71734518780.084100
5.85-8.278.30.09219.71241215000.09299.9
8.27-29.0567.70.07920.168228820.07997.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
BUSTER-TNT2.10.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 1.85→29.056 Å / Cor.coef. Fo:Fc: 0.9617 / Cor.coef. Fo:Fc free: 0.9584 / Occupancy max: 1 / Occupancy min: 0.3 / 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, CHLORIDE, GLYCEROL MODELED WERE PRESENT IN THE CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 3390 5.07 %RANDOM
Rwork0.1638 ---
obs0.1647 66923 99.86 %-
Displacement parametersBiso max: 114.12 Å2 / Biso mean: 37.2853 Å2 / Biso min: 15.58 Å2
Baniso -1Baniso -2Baniso -3
1-2.3149 Å20 Å20 Å2
2--2.3149 Å20 Å2
3----4.6298 Å2
Refine analyzeLuzzati coordinate error obs: 0.197 Å
Refinement stepCycle: LAST / Resolution: 1.85→29.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 151 656 4705
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2001SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes119HARMONIC2
X-RAY DIFFRACTIONt_gen_planes639HARMONIC5
X-RAY DIFFRACTIONt_it4328HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion564SEMIHARMONIC5
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_contact5368SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4328HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5895HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.8
X-RAY DIFFRACTIONt_other_torsion2.61
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1988 253 5.22 %
Rwork0.2022 4593 -
all0.202 4846 -
obs--99.86 %
Refinement TLS params.Method: refined / Origin x: 46.4263 Å / Origin y: 34.1448 Å / Origin z: 92.1478 Å
111213212223313233
T0.003 Å2-0.0163 Å2-0.0137 Å2--0.0606 Å2-0.0253 Å2---0.0332 Å2
L0.4324 °2-0.4019 °2-0.3179 °2-0.5564 °20.375 °2--0.3019 °2
S-0.0361 Å °-0.0899 Å °0.0049 Å °0.1398 Å °0.0204 Å °0.0192 Å °0.0544 Å °-0.0082 Å °0.0158 Å °
Refinement TLS groupSelection details: { A|32 - 534 }

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