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- PDB-2p58: Structure of the Yersinia pestis Type III secretion system needle... -

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Basic information

Entry
Database: PDB / ID: 2p58
TitleStructure of the Yersinia pestis Type III secretion system needle protein YscF in complex with its chaperones YscE/YscG
Components
  • Putative type III secretion protein YscE
  • Putative type III secretion protein YscF
  • Putative type III secretion protein YscG
KeywordsTRANSPORT PROTEIN/CHAPERONE / type III secretion system / needle protein / YscE / YscF / YscG / TRANSPORT PROTEIN-CHAPERONE COMPLEX
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / cell surface / extracellular region / cytoplasm
Similarity search - Function
Type III secretion system YscG / Bacterial type III secretion system chaperone protein / Type III secretion system, secretion protein E / Type III secretion system, cytoplasmic E component of needle / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / Immunoglobulin FC, subunit C / Tetratricopeptide repeat domain ...Type III secretion system YscG / Bacterial type III secretion system chaperone protein / Type III secretion system, secretion protein E / Type III secretion system, cytoplasmic E component of needle / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / Immunoglobulin FC, subunit C / Tetratricopeptide repeat domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Type 3 secretion system chaperone YscG / Type 3 secretion system needle filament protein / Type 3 secretion system chaperone YscE / Type 3 secretion system chaperone YscG / Type 3 secretion system needle filament protein / Type 3 secretion system chaperone YscE
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSun, P. / Austin, B.P. / Tropea, J.E. / Waugh, D.S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural characterization of the Yersinia pestis type III secretion system needle protein YscF in complex with its heterodimeric chaperone YscE/YscG.
Authors: Sun, P. / Tropea, J.E. / Austin, B.P. / Cherry, S. / Waugh, D.S.
History
DepositionMar 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative type III secretion protein YscE
B: Putative type III secretion protein YscF
C: Putative type III secretion protein YscG


Theoretical massNumber of molelcules
Total (without water)30,4503
Polymers30,4503
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-40.9 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.500, 94.540, 31.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative type III secretion protein YscE


Mass: 7673.239 Da / Num. of mol.: 1 / Fragment: YscE: Residues 10-63
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO-92, Biovar Orientalis / Gene: yscE, YPCD1.54, pCD29 / Plasmid: pBA1578 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q7ARI1, UniProt: O68692*PLUS
#2: Protein Putative type III secretion protein YscF


Mass: 9463.414 Da / Num. of mol.: 1 / Fragment: YscF: Residues 50-87
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO-92, Biovar Orientalis / Gene: yscF, YPCD1.55, pCD28 / Plasmid: pYscF2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q7ARI0, UniProt: O68691*PLUS
#3: Protein Putative type III secretion protein YscG


Mass: 13313.736 Da / Num. of mol.: 1 / Fragment: YscG: Residues 3-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO-92, Biovar Orientalis / Gene: yscG, YPCD1.56, pCD27 / Plasmid: pBA1578 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q7ARH9, UniProt: O68690*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.835 Å3/Da / Density % sol: 32.967 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium fluoride, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97928 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2006 / Details: mirror
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionRedundancy: 6.5 % / Av σ(I) over netI: 16.2 / Number: 136238 / Rmerge(I) obs: 0.101 / Χ2: 1.1 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 21105 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.885099.210.081.0736.4
3.083.8896.510.0851.0666.5
2.693.0810010.0961.0797
2.442.6910010.1161.0877.1
2.272.4499.910.131.1836.9
2.132.2795.510.151.0925.9
2.032.1310010.1881.017.1
1.942.0310010.261.1426.9
1.861.9499.910.3641.1256
1.81.8695.110.3691.1594.6
ReflectionResolution: 1.8→50 Å / Num. all: 21105 / Num. obs: 21105 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.101 / Χ2: 1.06 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 4.28 / Num. unique all: 1992 / Χ2: 1.139 / % possible all: 95.1

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.79 Å / D res low: 37.15 Å / FOM : 0.266 / FOM acentric: 0.287 / FOM centric: 0 / Reflection: 37531
Phasing MAD setR cullis: 0.748 / R cullis acentric: 0.713 / R cullis centric: 10 / R kraut: 0.051 / R kraut acentric: 0.053 / R kraut centric: 0.028 / Highest resolution: 1.79 Å / Lowest resolution: 37.15 Å / FOM : 0.273 / FOM acentric: 0.295 / FOM centric: 0 / Loc: 11.036 / Loc acentric: 10.958 / Loc centric: 12.109 / Power: 1.313 kW / Power acentric: 1.293 / Power centric: 1.497
Phasing MAD set shell

ID: fobs_FRIED / R cullis centric: 10 / FOM centric: 0

Resolution (Å)R cullisR cullis acentricR krautR kraut acentricR kraut centricFOM FOM acentricLocLoc acentricLoc centricPower (kW)Power acentricPower centric
3.58-37.150.7130.6560.0340.0360.0240.2990.35316.96316.9917.1131.5181.4861.682
2.84-3.580.7150.6830.0390.040.0280.3310.36312.53112.53712.5851.4861.4881.468
2.48-2.840.6890.6640.0460.0480.0310.3480.37510.17310.17510.1991.4761.4681.579
2.26-2.480.7240.70.0520.0530.0320.3230.3459.3729.3759.4011.351.3461.407
2.09-2.260.8010.7770.060.0620.0330.2630.289.4819.4829.4971.0981.0971.105
1.97-2.090.8340.8110.0720.0730.0350.2390.2529.2489.2519.2820.9870.9870.986
1.87-1.970.8630.8390.1040.1060.0480.1810.19110.10510.10710.1340.7890.7840.873
1.79-1.870.8640.8430.1220.1260.0470.1440.15110.1810.18210.2070.7110.710.736
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-13.709-24.446-1.086118.651
2-3.391-19.336-5.497219.491
3-4.718-0.168-13.206313.721
4-6.449-26.777-2.585421.841
5-9.978-34.925-0.1526.351
6-36.568-41.098-16.74631.181
7-17.506-11.229-0.64759.651
8-16.071-10.447-5.563839.211
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflection
3.58-37.150.30520.356604844
2.84-3.580.33090.362705016
2.48-2.840.34790.374405059
2.26-2.480.3150.336104779
2.09-2.260.25330.268304726
1.97-2.090.23150.244104794
1.87-1.970.16990.178904593
1.79-1.870.13090.13703720
Phasing dmDelta phi final: 38.29 / Delta phi initial: 55.48 / FOM : 0.806 / Mask type: RMS / Method: FLIP / Reflection: 39726
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
4.8-5017.2040.7282095
3.81-4.819.730.8862097
3.33-3.8127.5650.9062087
3.03-3.3327.6890.842089
2.81-3.0328.6080.8362104
2.64-2.8129.5140.8392071
2.51-2.6428.4510.8292099
2.4-2.5131.1510.8232092
2.31-2.436.0780.8182094
2.23-2.3139.850.8542059
2.16-2.2342.8490.7992138
2.1-2.1640.7560.7872070
2.04-2.144.2130.782107
1.99-2.0446.8640.7532080
1.95-1.9949.8830.7382082
1.91-1.9553.9970.7072107
1.87-1.9155.3570.7762057
1.83-1.8754.9480.7642076
1.8-1.8352.9090.8552122

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 2001 9.4 %random
Rwork0.1901 ---
all0.1901 20372 --
obs0.1901 20372 95.8 %-
Solvent computationBsol: 41.347 Å2
Displacement parametersBiso mean: 27.677 Å2
Baniso -1Baniso -2Baniso -3
1--8.365 Å20 Å20 Å2
2--3.483 Å20 Å2
3---4.883 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 0 227 1859
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4761.5
X-RAY DIFFRACTIONc_scbond_it2.7522
X-RAY DIFFRACTIONc_mcangle_it2.2242
X-RAY DIFFRACTIONc_scangle_it4.1692.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.274 174 -
Rwork0.221 --
obs-1992 87.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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