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- PDB-5k93: PapD wild-type chaperone -

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Basic information

Entry
Database: PDB / ID: 5k93
TitlePapD wild-type chaperone
ComponentsChaperone protein PapD
KeywordsCHAPERONE
Function / homology
Function and homology information


chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space
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
Chaperone protein PapD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsSarowar, S. / Li, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008468 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM062987 United States
CitationJournal: J.Bacteriol. / Year: 2016
Title: The Escherichia coli P and Type 1 Pilus Assembly Chaperones PapD and FimC Are Monomeric in Solution.
Authors: Sarowar, S. / Hu, O.J. / Werneburg, G.T. / Thanassi, D.G. / Li, H.
History
DepositionMay 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein PapD
B: Chaperone protein PapD


Theoretical massNumber of molelcules
Total (without water)50,3212
Polymers50,3212
Non-polymers00
Water0
1
A: Chaperone protein PapD


Theoretical massNumber of molelcules
Total (without water)25,1601
Polymers25,1601
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chaperone protein PapD


Theoretical massNumber of molelcules
Total (without water)25,1601
Polymers25,1601
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.129, 70.989, 93.050
Angle α, β, γ (deg.)90.00, 102.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chaperone protein PapD /


Mass: 25160.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papD / Production host: Escherichia coli (E. coli) / References: UniProt: P15319

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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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citric acid, pH 3.6, 25% PEG-3350

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Data collection

DiffractionMean temperature: 277.15 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0749 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0749 Å / Relative weight: 1
ReflectionResolution: 2.7→49.2 Å / Num. obs: 13917 / % possible obs: 96.8 % / Redundancy: 3.7 % / Net I/σ(I): 23.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.7→49.19 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.872 / SU B: 14.671 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R: 1.432 / ESU R Free: 0.375 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27858 743 5.1 %RANDOM
Rwork0.22047 ---
obs0.22342 13917 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.807 Å2
Baniso -1Baniso -2Baniso -3
1--3.85 Å20 Å20.52 Å2
2--1.92 Å20 Å2
3---1.66 Å2
Refinement stepCycle: 1 / Resolution: 2.7→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 0 0 3330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023398
X-RAY DIFFRACTIONr_bond_other_d0.0020.023262
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9824608
X-RAY DIFFRACTIONr_angle_other_deg0.81937536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7345416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07724.286154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.48615600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1371526
X-RAY DIFFRACTIONr_chiral_restr0.0860.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213814
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02740
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.696→2.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 47 -
Rwork0.333 960 -
obs--92.73 %

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