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- PDB-4gpv: Crystal structure of a putative cell adhesion protein (BACEGG_005... -

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Basic information

Entry
Database: PDB / ID: 4gpv
TitleCrystal structure of a putative cell adhesion protein (BACEGG_00536) from Bacteroides eggerthii DSM 20697 at 1.67 A resolution
Componentsputative cell adhesion protein
KeywordsCELL ADHESION / Major fimbrial subunit protein (FimA) / PF06321 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyImmunoglobulin-like - #3690 / Immunoglobulin-like - #2580 / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesBacteroides eggerthii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 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
DepositionAug 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Apr 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 1.4Feb 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 1.5Nov 20, 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: putative cell adhesion protein
B: putative cell adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8154
Polymers72,5712
Non-polymers2442
Water13,926773
1
A: putative cell adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4072
Polymers36,2851
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: putative cell adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4072
Polymers36,2851
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.060, 61.488, 64.112
Angle α, β, γ (deg.)109.610, 103.020, 90.900
Int Tables number1
Space group name H-MP1

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Components

#1: Protein putative cell adhesion protein


Mass: 36285.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii (bacteria) / Strain: DSM 20697 / Gene: BACEGG_00536 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B7ADR8
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (21-367) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (21-367) 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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M sodium acetate, 30.0% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97903
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 3, 2012
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.67→40.625 Å / Num. obs: 70659 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.835 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.67-1.730.762227930708694.9
1.73-1.80.481328497723095.7
1.8-1.880.324.427352696895.8
1.88-1.980.189728170721195.4
1.98-2.10.1279.926987692595.4
2.1-2.270.08813.529125750495.7
2.27-2.490.0716.726342683395.1
2.49-2.850.0492226603698093
2.85-3.590.03231.326253689791.7
3.590.02837.926787702493.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 1.67→40.625 Å / Cor.coef. Fo:Fc: 0.9621 / Cor.coef. Fo:Fc free: 0.9519 / 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. TRIS (TRS) MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS)
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 3565 5.05 %RANDOM
Rwork0.1599 ---
obs0.1613 70657 94.78 %-
Displacement parametersBiso max: 141.52 Å2 / Biso mean: 32.7141 Å2 / Biso min: 13.62 Å2
Baniso -1Baniso -2Baniso -3
1--6.7945 Å2-0.8128 Å2-0.3955 Å2
2--6.2677 Å20.247 Å2
3---0.5268 Å2
Refine analyzeLuzzati coordinate error obs: 0.228 Å
Refinement stepCycle: LAST / Resolution: 1.67→40.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4761 0 16 773 5550
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2304SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes126HARMONIC2
X-RAY DIFFRACTIONt_gen_planes781HARMONIC5
X-RAY DIFFRACTIONt_it5040HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion747SEMIHARMONIC5
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_contact6285SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5040HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6919HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.84
X-RAY DIFFRACTIONt_other_torsion2.45
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2272 247 4.72 %
Rwork0.2238 4987 -
all0.2239 5234 -
obs--94.78 %
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)
10.9172-0.93820.08652.20140.08610.69060.00060.0244-0.04320.0471-0.02360.0069-0.02360.05110.023-0.07250.00920.006-0.06530.0053-0.073462.516289.8645-18.1665
20.45310.4060.07171.83290.21610.42050.00120.00250.02-0.09420.01810.14970.04680.0419-0.01940.002-0.0133-0.0057-0.07960.014-0.067938.853560.98519.163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|28 - 363}A28 - 363
2X-RAY DIFFRACTION2{B|28 - 363}B28 - 363

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