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- PDB-3r4r: Crystal structure of a fimbrial assembly protein (BDI_3522) from ... -

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Basic information

Entry
Database: PDB / ID: 3r4r
TitleCrystal structure of a fimbrial assembly protein (BDI_3522) from Parabacteroides distasonis ATCC 8503 at 2.38 A resolution
Componentshypothetical fimbrial assembly protein
KeywordsCELL ADHESION / transthyretin-like (also known as prealbumin-like) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-biology
Function / homologyImmunoglobulin-like - #2590 / Immunoglobulin-like - #2580 / Major fimbrial subunit protein, N-terminal / Major fimbrial subunit protein (FimA) / pilus / Immunoglobulin-like / Sandwich / Mainly Beta / Putative fimbrium tip subunit Fim1F
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.38 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
DepositionMar 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 24, 2014Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical fimbrial assembly protein
B: hypothetical fimbrial assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,37110
Polymers65,8072
Non-polymers5658
Water1,42379
1
A: hypothetical fimbrial assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4068
Polymers32,9031
Non-polymers5027
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: hypothetical fimbrial assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9652
Polymers32,9031
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.983, 84.801, 113.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical fimbrial assembly protein


Mass: 32903.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_3522 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LHQ9
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


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


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 24-318 OF 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.4
Details: 2.32M ammonium sulfate, 0.2M lithium sulfate, 0.1M CAPS pH 10.4, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97954,0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 5, 2009 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979541
30.979361
ReflectionResolution: 2.38→36.492 Å / Num. obs: 28498 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.474 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.38-2.460.8841.69128260997.4
2.46-2.560.6662.19866281797.6
2.56-2.680.492.810233290598.1
2.68-2.820.3483.99923278598
2.82-30.2196.210261286598.6
3-3.230.1379.39983282698.7
3.23-3.550.07815.79888282698.8
3.55-4.060.04923.69704284197.9
4.06-5.10.02933.89573283296.8
5.10.0243810315306897.2

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Phasing

PhasingMethod: MAD

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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
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.38→36.492 Å / Cor.coef. Fo:Fc: 0.9068 / Cor.coef. Fo:Fc free: 0.9049 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. SULFATE (SO4) FROM THE CRYSTALLIZATION CONDITION AND ETHYLENE GLYCOL (EDO), USED AS A CRYOPROTECTANT HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. NCS RESTRAINTS WERE APPLIED USING BUSTERS LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 6. CHAIN TRACING WAS PERFORMED FROM MAD DATA COLLECTED ON A CRYSTAL THAT DIFFRACTED TO 2.64 ANGSTROMS RESOLUTION. THE RESULTING TRACE WAS REFINED AGAINST DATA COLLECTED FROM A SECOND CRYSTAL THAT DIFFRACTED TO 2.38 ANGSTROMS RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1448 5.09 %RANDOM
Rwork0.2256 ---
obs0.2266 28454 --
Displacement parametersBiso max: 181.91 Å2 / Biso mean: 75.2448 Å2 / Biso min: 21.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.7873 Å20 Å20 Å2
2--11.0242 Å20 Å2
3----12.8115 Å2
Refinement stepCycle: LAST / Resolution: 2.38→36.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 34 79 4155
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1867SINUSOIDAL12
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes605HARMONIC5
X-RAY DIFFRACTIONt_it4159HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion582SEMIHARMONIC5
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_contact4482SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4159HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5656HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion1.72
LS refinement shellResolution: 2.38→2.47 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3068 157 5.43 %
Rwork0.2268 2735 -
all0.2311 2892 -
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)
17.1519-1.06860.23591.3322-0.20282.0695-0.3089-0.7844-0.24180.16350.2151-0.15440.1398-0.1950.0938-0.3339-0.02450.00060.104-0.0341-0.249236.096314.962667.4677
29.30340.48042.01561.58690.58035.01730.43220.9356-0.4951-0.1006-0.0809-0.20160.1301-0.3456-0.3513-0.35950.1973-0.03580.03260.1672-0.332138.976417.0838100.148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|32 - A|315 }A32 - 315
2X-RAY DIFFRACTION2{ B|34 - B|317 }B34 - 317

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