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- PDB-4k4k: Crystal structure of a putative cell adhesion protein (BACUNI_006... -

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Basic information

Entry
Database: PDB / ID: 4k4k
TitleCrystal structure of a putative cell adhesion protein (BACUNI_00621) from Bacteroides uniformis ATCC 8492 at 1.67 A resolution
ComponentsPutative cell adhesion protein
KeywordsCELL ADHESION / Fimbrillin-like protein / PF13149 family / DUF3988 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Immunoglobulin-like - #2630 / Fimbrillin-like / Fimbrillin-like 1, N-terminal / Fimbrillin-like 1 / Fimbrillin-like / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative fimbrium subunit Fim1C
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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
DepositionApr 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: 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)59,6754
Polymers59,6042
Non-polymers712
Water8,503472
1
A: Putative cell adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8382
Polymers29,8021
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative cell adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8382
Polymers29,8021
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.398, 140.225, 53.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative cell adhesion protein


Mass: 29802.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: ATCC 8492 / Gene: BACUNI_00621 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7UZ95
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (23-303) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (23-303) 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: 1.87 Å3/Da / Density % sol: 34.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40% polyethylene glycol 600, 0.1M sodium citrate pH 5.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97941,0.97874
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979411
30.978741
ReflectionResolution: 1.67→45.32 Å / Num. obs: 52130 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.66 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.67-1.713.80.9561.714303380499.6
1.71-1.763.70.7492.113762370199.3
1.76-1.813.70.5662.913218360498.8
1.81-1.873.40.4273.512027350598.9
1.87-1.933.60.3264.712301339699.1
1.93-23.80.2356.612747334699.6
2-2.073.80.1718.511965316499.3
2.07-2.163.80.13510.311619309599.4
2.16-2.253.70.11711.810894294199.4
2.25-2.363.60.113.510100280898.1
2.36-2.493.50.08415.39472268698.8
2.49-2.643.80.07218.79812255899.7
2.64-2.823.80.06121.89208244899.8
2.82-3.053.70.046288354224999.3
3.05-3.343.50.03534.97303207198.2
3.34-3.733.40.02943.16240182196.7
3.73-4.313.70.026506257168499.2
4.31-5.283.60.024535196144799.1
5.28-7.473.30.02944.53666112097.4
7.47-45.323.50.02750.3238868298.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.67→45.32 Å / Cor.coef. Fo:Fc: 0.9582 / Cor.coef. Fo:Fc free: 0.9475 / 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. CL MODELED ARE PRESENT IN CRYSTALLIZATION CONDITION. 5.NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 2658 5.1 %RANDOM
Rwork0.1866 ---
obs0.1881 52074 98.84 %-
Displacement parametersBiso max: 121.59 Å2 / Biso mean: 32.0553 Å2 / Biso min: 7.77 Å2
Baniso -1Baniso -2Baniso -3
1--4.9817 Å20 Å20 Å2
2--3.3333 Å20 Å2
3---1.6485 Å2
Refine analyzeLuzzati coordinate error obs: 0.225 Å
Refinement stepCycle: LAST / Resolution: 1.67→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 2 472 4254
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1882SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes110HARMONIC2
X-RAY DIFFRACTIONt_gen_planes631HARMONIC5
X-RAY DIFFRACTIONt_it4065HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion590SEMIHARMONIC5
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_contact5000SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4065HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5589HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion2.4
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2672 209 5.51 %
Rwork0.2256 3582 -
all0.2278 3791 -
obs--98.84 %
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)
10.32040.2833-0.32562.9637-0.71190.8065-0.0029-0.0191-0.05480.2868-0.024-0.04070.15290.10070.02690.00070.0082-0.013-0.10630.004-0.0631-18.9234-16.545419.8152
20.22720.20910.26523.01890.6240.61620.04690.00380.04150.1749-0.02680.0094-0.1093-0.0688-0.0202-0.03810.00060.0318-0.0821-0.0022-0.0309-10.201517.1156-7.0007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|28 - 291}A28 - 291
2X-RAY DIFFRACTION2{B|31 - 291}B31 - 291

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