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- PDB-4q98: Crystal structure of a fimbrilin (fimA) from Porphyromonas gingiv... -

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Basic information

Entry
Database: PDB / ID: 4q98
TitleCrystal structure of a fimbrilin (fimA) from Porphyromonas gingivalis W83 at 1.30 A resolution (PSI Community Target, Nakayama)
ComponentsMajor fimbrial subunit protein
KeywordsCELL ADHESION / PF06321 / Type IV / PF15495 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


pilus / cell outer membrane / cell adhesion / structural molecule activity
Similarity search - Function
Porphyromonas gingivalis fimbrillin protein / : / FimA4 pilin C-terminal domain / Major fimbrial subunit protein type IV, Fimbrillin, C-terminal / Major fimbrial subunit protein, N-terminal / Major fimbrial subunit protein (FimA) / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Major fimbrium subunit FimA type-4
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 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 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Apr 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 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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: Major fimbrial subunit protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3422
Polymers39,3191
Non-polymers231
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.398, 67.641, 65.576
Angle α, β, γ (deg.)90.000, 90.470, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Major fimbrial subunit protein / Fimbrillin / Fimbrilin


Mass: 39319.156 Da / Num. of mol.: 1 / Fragment: UNP residues 3-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: ATCC BAA-308 / W83 / Gene: fimA, PG_2132 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: P59914
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 21-388 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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30.00% polyethylene glycol 6000, 0.1M HEPES pH 7.0, 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: 0.91837,0.97849
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2014
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
20.978491
ReflectionResolution: 1.3→47.082 Å / Num. obs: 73835 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.99 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 15.19
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.3-1.370.4362.2224448400174.5
1.37-1.420.3443.1213076540196.4
1.42-1.490.264.4270297939199.2
1.49-1.560.1875.9215506507197.8
1.56-1.660.1368.1258687612198.9
1.66-1.790.09211.5255577490199
1.79-1.970.05618244347309197.9
1.97-2.260.03926.3261277535198.8
2.26-2.840.03331.7245547228197.9
2.84-47.0820.02341.4243057339196.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMAC5.8.0069refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.3→47.082 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.975 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.717 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.047
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. A SODIUM ION (NA) MODELED WAS PRESENT IN CRYSTALLIZATION CONDITIONS. 4. THE DENSITIES FOR LOOP REGION (45-49) ARE POOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.1561 3704 5 %RANDOM
Rwork0.1186 ---
obs0.1205 73813 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.39 Å2 / Biso mean: 19.0056 Å2 / Biso min: 7.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0.32 Å2
2--0.18 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.3→47.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 1 609 3269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222982
X-RAY DIFFRACTIONr_bond_other_d0.0010.022803
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9564136
X-RAY DIFFRACTIONr_angle_other_deg0.84436508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6515432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.72826.815135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.78115483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.435154
X-RAY DIFFRACTIONr_chiral_restr0.0920.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213609
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02662
X-RAY DIFFRACTIONr_mcbond_it2.2421.4571526
X-RAY DIFFRACTIONr_mcbond_other2.2381.4541525
X-RAY DIFFRACTIONr_mcangle_it2.752.1991929
X-RAY DIFFRACTIONr_rigid_bond_restr3.08435785
X-RAY DIFFRACTIONr_sphericity_free27.2255361
X-RAY DIFFRACTIONr_sphericity_bonded9.57555953
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 197 -
Rwork0.233 3686 -
all-3883 -
obs--68.08 %

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