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- PDB-4wo7: Crystal Structure of PrsA from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 4wo7
TitleCrystal Structure of PrsA from Bacillus subtilis
ComponentsFoldase protein PrsA
KeywordsISOMERASE / foldase / prolyl isomerase / protein secretion / Gram-positive
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / protein folding / membrane raft / plasma membrane
Similarity search - Function
Foldase protein PrsA / PPIC-type PPIASE domain / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 ...Foldase protein PrsA / PPIC-type PPIASE domain / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Foldase protein PrsA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.63 Å
AuthorsJakob, R.P. / Maier, T.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3_152989 Switzerland
Swiss National Science FoundationCRSII3_147646 Switzerland
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Dimeric Structure of the Bacterial Extracellular Foldase PrsA.
Authors: Jakob, R.P. / Koch, J.R. / Burmann, B.M. / Schmidpeter, P.A. / Hunkeler, M. / Hiller, S. / Schmid, F.X. / Maier, T.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Feb 18, 2015Group: Database references
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / pdbx_audit_support / pdbx_validate_close_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Foldase protein PrsA
B: Foldase protein PrsA


Theoretical massNumber of molelcules
Total (without water)59,9542
Polymers59,9542
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-24 kcal/mol
Surface area30480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.290, 87.680, 234.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Foldase protein PrsA


Mass: 29977.182 Da / Num. of mol.: 2 / Fragment: UNP residues 21-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: prsA, BSU09950 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24327, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 17 % PEG2000MME, 0.1M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.36246 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36246 Å / Relative weight: 1
ReflectionResolution: 2.63→117 Å / Num. obs: 21428 / % possible obs: 98.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.7
Reflection shellResolution: 2.63→2.79 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.6 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1779)refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.63→54.364 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1100 5.14 %Random
Rwork0.2263 ---
obs0.2275 21421 98.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→54.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 0 35 4121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054132
X-RAY DIFFRACTIONf_angle_d1.045512
X-RAY DIFFRACTIONf_dihedral_angle_d14.5051624
X-RAY DIFFRACTIONf_chiral_restr0.04607
X-RAY DIFFRACTIONf_plane_restr0.003695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6302-2.74990.36471260.4142316X-RAY DIFFRACTION92
2.7499-2.89480.39731390.34932539X-RAY DIFFRACTION100
2.8948-3.07620.31371380.32632515X-RAY DIFFRACTION100
3.0762-3.31370.33871400.29672561X-RAY DIFFRACTION100
3.3137-3.64710.29231580.25592528X-RAY DIFFRACTION100
3.6471-4.17460.24961460.22762550X-RAY DIFFRACTION100
4.1746-5.25890.22541350.19632590X-RAY DIFFRACTION100
5.2589-54.37530.20641180.1912722X-RAY DIFFRACTION99
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)
14.8787-2.56241.54275.1226-0.79883.12170.28910.85450.0527-0.7555-0.2211-0.29730.25090.1876-0.05440.55740.04070.06810.6583-0.05210.5221-4.5356-3.529276.6425
22.41651.0281-2.58743.224-1.2313.85040.4373-0.45940.36290.316-0.1445-0.1248-0.96590.6176-0.26960.8782-0.1149-0.12780.8015-0.06730.5464.925922.508170.5746
34.9835-1.10282.75681.8702-0.97554.63880.1776-0.55540.07450.26420.0761-0.26190.1656-0.2333-0.13920.62220.0430.0430.5947-0.05340.70333.326-9.426797.3079
42.6751.29540.0632.090.84781.61720.3384-0.10950.2976-0.26750.1261-0.4999-0.47580.2289-0.36120.95370.09060.2170.81210.06720.919126.18325.6285102.6889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 259 )
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 99 )
4X-RAY DIFFRACTION4chain 'B' and (resid 100 through 259 )

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