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- PDB-4a0e: Crystal structure of the cytoplasmic N-terminal domain of Yersini... -

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Basic information

Entry
Database: PDB / ID: 4a0e
TitleCrystal structure of the cytoplasmic N-terminal domain of Yersinia pestis YscD
ComponentsTYPE III SECRETION PROTEIN
KeywordsTRANSPORT PROTEIN / SAD PHASING / TYPE III SECRETION SYSTEM
Function / homology
Function and homology information


: / Uncharacterised protein Y4YQ C-terminal domain / Yop protein translocation protein D, periplasmic domain / : / : / YscD/CdsD-like Bon-like domain 1 / YscD/CdsD-like Bon-like domain 3 / YscD/CdsD-like Bon-like domain 2 / Type III secretion system YscD/HrpQ / YscD, cytoplasmic domain ...: / Uncharacterised protein Y4YQ C-terminal domain / Yop protein translocation protein D, periplasmic domain / : / : / YscD/CdsD-like Bon-like domain 1 / YscD/CdsD-like Bon-like domain 3 / YscD/CdsD-like Bon-like domain 2 / Type III secretion system YscD/HrpQ / YscD, cytoplasmic domain / Inner membrane component of T3SS, cytoplasmic domain / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Type III secretion protein / Type III secretion protein
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.042 Å
AuthorsLountos, G.T. / Tropea, J.E. / Waugh, D.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of the Cytoplasmic Domain of Yersinia Pestis Yscd, an Essential Component of the Type III Secretion System
Authors: Lountos, G.T. / Tropea, J.E. / Waugh, D.S.
History
DepositionSep 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYPE III SECRETION PROTEIN
B: TYPE III SECRETION PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,9672
Polymers26,9672
Non-polymers00
Water1,58588
1
A: TYPE III SECRETION PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,4831
Polymers13,4831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TYPE III SECRETION PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,4831
Polymers13,4831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.227, 118.227, 118.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

#1: Protein TYPE III SECRETION PROTEIN / YSCD


Mass: 13483.413 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 2-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PJT173 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q1BZW5, UniProt: Q56975*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST THREE GLYCINES ARE NON-NATIVE RESIDUES REMAINING AFTER TAG CLEAVAGE

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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: 2.56 Å3/Da / Density % sol: 51.9 % / Description: NONE
Crystal growpH: 8.5
Details: 0.085M TRIS HCL PH 8.5, 25.5% (W/V) PEG 4000, 0.17M NA ACETATE, 15% (V/V) GLYCEROL, 10 MM TCEP HYDROCHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Jun 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 18490 / % possible obs: 98.9 % / Observed criterion σ(I): 2.1 / Redundancy: 5.1 % / Biso Wilson estimate: 46.43 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 41.6
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.042→39.409 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2558 895 5 %
Rwork0.2106 --
obs0.2129 17908 96.45 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.686 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.042→39.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 0 88 1738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071690
X-RAY DIFFRACTIONf_angle_d1.0852310
X-RAY DIFFRACTIONf_dihedral_angle_d14.55614
X-RAY DIFFRACTIONf_chiral_restr0.072270
X-RAY DIFFRACTIONf_plane_restr0.005300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0417-2.16960.41851410.34522598X-RAY DIFFRACTION91
2.1696-2.33720.34741410.2922694X-RAY DIFFRACTION94
2.3372-2.57230.32811440.25322807X-RAY DIFFRACTION97
2.5723-2.94440.27611500.23552871X-RAY DIFFRACTION99
2.9444-3.70920.26721560.19632950X-RAY DIFFRACTION100
3.7092-39.41630.21271630.1863093X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 28.8948 Å / Origin y: -14.1843 Å / Origin z: -46.6411 Å
111213212223313233
T0.2382 Å20.0264 Å2-0.0189 Å2-0.3165 Å20.0721 Å2--0.2653 Å2
L0.7862 °2-0.181 °2-0.2975 °2-0.4107 °20.2084 °2--0.3162 °2
S-0.1141 Å °-0.2051 Å °0 Å °0.0465 Å °0.0453 Å °0.0018 Å °-0.0011 Å °0.0413 Å °0.0573 Å °
Refinement TLS groupSelection details: ALL

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