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- PDB-3t2l: Crystal structure of a Putative cell adhesion protein (BF1858) fr... -

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Basic information

Entry
Database: PDB / ID: 3t2l
TitleCrystal structure of a Putative cell adhesion protein (BF1858) from Bacteroides fragilis NCTC 9343 at 2.33 A resolution
ComponentsPutative cell adhesion protein
KeywordsCELL ADHESION / Prealbumin-like fold / 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 fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 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
DepositionJul 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cell adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7206
Polymers34,3731
Non-polymers3475
Water2,702150
1
A: Putative cell adhesion protein
hetero molecules

A: Putative cell adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,43912
Polymers68,7452
Non-polymers69410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area6570 Å2
ΔGint-61 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.285, 87.285, 101.476
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative cell adhesion protein


Mass: 34372.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF1858 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5LE95
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 21-327) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 21-327) 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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 1.2M sodium dihydrogen phosphate, 0.8M di-potassium hydrogen phosphate, 0.2M lithium sulfate, 0.1M CAPS pH 10.5, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97907
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 6, 2011
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: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.33→28.571 Å / Num. obs: 19607 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 14.52 % / Biso Wilson estimate: 54.212 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22.78
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.33-2.410.9452.67272343542199.7
2.41-2.510.7663.2295263835199.7
2.51-2.620.5724.3273643567199.7
2.62-2.760.4036.1291253785199.8
2.76-2.930.2549.1282533678199.8
2.93-3.160.13915.8286793769199.9
3.16-3.480.08224.5286463733199.9
3.48-3.980.04640.3285453695199.9
3.98-50.03157.32813436701100
5-28.570.02363.8291153759199.1

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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-TNT2.8.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.33→28.571 Å / Cor.coef. Fo:Fc: 0.9428 / Cor.coef. Fo:Fc free: 0.9226 / 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. GLYCEROL (GOL) AND CHLORIDE MODELED ARE PRESENT IN PROTEIN BUFFER/CRYO BUFFERS. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 993 5.09 %RANDOM
Rwork0.1754 ---
obs0.1775 19509 --
Displacement parametersBiso max: 181.58 Å2 / Biso mean: 57.8296 Å2 / Biso min: 22.35 Å2
Baniso -1Baniso -2Baniso -3
1--7.0497 Å20 Å20 Å2
2---7.0497 Å20 Å2
3---14.0994 Å2
Refinement stepCycle: LAST / Resolution: 2.33→28.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 20 150 2326
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1045SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes325HARMONIC5
X-RAY DIFFRACTIONt_it2263HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion307SEMIHARMONIC5
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_contact2387SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2263HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3085HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.92
X-RAY DIFFRACTIONt_other_torsion2.63
LS refinement shellResolution: 2.33→2.46 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2409 152 5.42 %
Rwork0.1949 2651 -
all0.1973 2803 -
Refinement TLS params.Method: refined / Origin x: -0.6245 Å / Origin y: 26.1557 Å / Origin z: 3.4238 Å
111213212223313233
T-0.1047 Å2-0.0714 Å20.0274 Å2--0.0669 Å20.0233 Å2---0.086 Å2
L1.1561 °20.3468 °2-1.6269 °2-0.5952 °2-0.7913 °2--3.6932 °2
S-0.0771 Å °-0.041 Å °-0.0613 Å °-0.0552 Å °0.0325 Å °0.0864 Å °0.2819 Å °-0.2186 Å °0.0446 Å °
Refinement TLS groupSelection details: { A|36 - 316 }

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