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- PDB-3liu: Crystal structure of Putative cell adhesion protein (YP_001304840... -

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Basic information

Entry
Database: PDB / ID: 3liu
TitleCrystal structure of Putative cell adhesion protein (YP_001304840.1) from Parabacteroides distasonis ATCC 8503 at 2.05 A resolution
ComponentsPutative cell adhesion protein
KeywordsCELL ADHESION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Immunoglobulin-like - #3160 / Immunoglobulin-like - #3690 / Major fimbrial subunit protein, N-terminal / Major fimbrial subunit protein (FimA) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 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
DepositionJan 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 22, 2020Group: Database references / Category: citation / citation_author
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
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 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
B: Putative cell adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,10412
Polymers87,4422
Non-polymers66110
Water10,575587
1
A: Putative cell adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8493
Polymers43,7211
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative cell adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2559
Polymers43,7211
Non-polymers5348
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.372, 101.934, 130.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 5 / Auth seq-ID: 33 - 412 / Label seq-ID: 14 - 393

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative cell adhesion protein / Putative fimbrilin


Mass: 43721.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_3517 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LHQ4

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Non-polymers , 5 types, 597 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 21-421) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 21-421) 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1600M ammonium sulfate, 20.1000% polyethylene glycol 4000, 20.0000% Glycerol, 0.1M sodium acetate pH 4.0, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97939,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 5, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979391
30.979221
ReflectionResolution: 2.05→47.493 Å / Num. obs: 54734 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.062 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.91
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.05-2.120.7292.1189445160199.8
2.12-2.210.5462.8211075721199.9
2.21-2.310.4353.5197755379199.7
2.31-2.430.3544.2196905332199.9
2.43-2.580.2845.1197835373199.9
2.58-2.780.2076.9202215470199.8
2.78-3.060.12810.4201515478199.9
3.06-3.50.06917200305475199.9
3.5-4.40.04325.5200685529199.7
4.4-47.4930.03429.9204225801198.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→47.493 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 8.323 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.16
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. ETHYLENE GLYCOL (EDO), GLYCEROL (GOL) AND SULFATE (SO4) MODELED WERE PRESENT IN CRYSTLLIZATION/CRYO CONDITIONS. CHLORIDE (CL) MODELED WAS PRESENT IN THE PROTEIN BUFFER. 5. CIS-PEPTIDE (323-324) IS SUPPORTED BY CLEAR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2786 5.1 %RANDOM
Rwork0.17 ---
obs0.173 54675 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.79 Å2 / Biso mean: 20.807 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5651 0 39 587 6277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225869
X-RAY DIFFRACTIONr_bond_other_d0.0020.023750
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9678010
X-RAY DIFFRACTIONr_angle_other_deg0.89639299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86226.341246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90815944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.572156
X-RAY DIFFRACTIONr_chiral_restr0.0950.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021065
X-RAY DIFFRACTIONr_mcbond_it1.86833733
X-RAY DIFFRACTIONr_mcbond_other0.77431528
X-RAY DIFFRACTIONr_mcangle_it2.99756056
X-RAY DIFFRACTIONr_scbond_it4.73182136
X-RAY DIFFRACTIONr_scangle_it6.789111941
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2168MEDIUM POSITIONAL0.30.5
2408LOOSE POSITIONAL0.55
2168MEDIUM THERMAL1.462
2408LOOSE THERMAL1.4310
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 208 -
Rwork0.24 3746 -
all-3954 -
obs--99.62 %
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)
10.2802-0.058-0.1951.08620.43510.71730.00340.0149-0.0118-0.0846-0.0051-0.0045-0.0615-0.01610.00160.00870.0016-0.00050.04870.01120.009932.5536.888658.7371
20.0185-0.0762-0.01520.59370.621.16790.0160.0060.0161-0.07440.0203-0.0646-0.06810.0629-0.03630.0423-0.00780.04940.04440.01020.075960.734636.483137.8813
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 412
2X-RAY DIFFRACTION2B30 - 412

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