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- PDB-5ghu: Crystal structure of YadV chaperone at 1.63 Angstrom -

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Basic information

Entry
Database: PDB / ID: 5ghu
TitleCrystal structure of YadV chaperone at 1.63 Angstrom
ComponentsProbable fimbrial chaperone YadV
KeywordsCHAPERONE / CU chaperone / fimbriae / pilin
Function / homology
Function and homology information


pilus organization / chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion
Similarity search - Function
Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Immunoglobulins ...Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / TRIETHYLENE GLYCOL / Probable fimbrial chaperone YadV
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsPandey, N.K. / Bhavesh, N.S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyBT/PR6400/BRB/10/113 India
CitationJournal: Febs Lett. / Year: 2020
Title: Crystal structure of the usher chaperone YadV reveals a monomer with the proline lock in closed conformation suggestive of an intermediate state.
Authors: Pandey, N.K. / Verma, G. / Kushwaha, G.S. / Suar, M. / Bhavesh, N.S.
History
DepositionJun 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity_name_com / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable fimbrial chaperone YadV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8366
Polymers24,4861
Non-polymers3505
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-9 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.280, 127.560, 45.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable fimbrial chaperone YadV


Mass: 24485.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ecpD / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): codonplus / References: UniProt: P33128

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Non-polymers , 5 types, 254 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M ammonium sulfate, 0.1 M sodium acetate, 0.3 M sodium formate, 30% PEG 400
PH range: 4.6 - 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.63→78.838 Å / Num. all: 36961 / Num. obs: 36961 / % possible obs: 99.5 % / Redundancy: 13.1 % / Rpim(I) all: 0.017 / Rrim(I) all: 0.064 / Rsym value: 0.06 / Net I/av σ(I): 6.8 / Net I/σ(I): 21.6 / Num. measured all: 485800
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.63-1.7212.20.5111.46410552580.1540.5520.5114.498.7
1.72-1.8212.40.3012.46216550270.090.3230.3017.499
1.82-1.9512.50.2013.55914247300.0590.2140.20111.599.4
1.95-2.112.80.1225.45709844480.0360.130.12218.299.9
2.1-2.3113.40.0966.75542141260.0280.1020.09623.5100
2.31-2.5813.90.0738.65174337260.0210.0770.07328.1100
2.58-2.9814.20.06394709633180.0180.0660.06335.2100
2.98-3.6414.30.0737.94031328220.020.0770.07343.4100
3.64-5.1514.20.0319.23166422360.0090.0320.0347.3100
5.15-20.84213.40.02818.81705312700.0080.0310.02844.298.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.97 Å22.01 Å
Translation1.97 Å22.01 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata collection
SCALA3.3.21data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
iMOSFLMdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ME0, 1KLF, 3F65

3me0

1klf

3f65


Resolution: 1.63→22.009 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.63 / Stereochemistry target values: ML / Details: 3 UNMODELLED BLOBS AT SYMMETRY POSITIONS
RfactorNum. reflection% reflection
Rfree0.1863 1834 4.96 %
Rwork0.1677 35127 -
obs0.1686 36961 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.36 Å2 / Biso mean: 35.6368 Å2 / Biso min: 14.41 Å2
Refinement stepCycle: final / Resolution: 1.63→22.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 44 249 1843
Biso mean--66.47 42.08 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161626
X-RAY DIFFRACTIONf_angle_d1.592205
X-RAY DIFFRACTIONf_chiral_restr0.087245
X-RAY DIFFRACTIONf_plane_restr0.01283
X-RAY DIFFRACTIONf_dihedral_angle_d12.584597
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.63-1.67410.24791490.19522624277399
1.6741-1.72330.21211390.17362640277998
1.7233-1.77890.18121240.16922624274898
1.7789-1.84250.19911380.15992675281399
1.8425-1.91620.15931290.16632689281899
1.9162-2.00330.21361590.158726702829100
2.0033-2.10890.17561420.155926792821100
2.1089-2.24090.20221110.173527222833100
2.2409-2.41370.19841560.172927112867100
2.4137-2.65620.19611600.179326962856100
2.6562-3.03970.17751480.176427352883100
3.0397-3.82650.20051270.165227852912100
3.8265-22.01070.16511520.160828773029100
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)
10.629-0.714-0.20522.6153-0.03941.7644-0.0196-0.10840.12780.11690.0873-0.0526-0.78510.0801-0.06240.4585-0.01240.00290.1937-0.03640.230423.602454.808114.2463
21.85110.06380.56151.022-0.24681.52840.0282-0.2207-0.1076-0.0230.05150.13750.054-0.2132-0.05560.15870.0009-0.00930.210.00450.204312.520929.861617.6974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 123 )A1 - 123
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 222 )A124 - 222

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