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- PDB-3gr1: Periplasmic domain of the T3SS inner membrane protein PrgH from S... -

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Basic information

Entry
Database: PDB / ID: 3gr1
TitlePeriplasmic domain of the T3SS inner membrane protein PrgH from S.typhimurium (fragment 170-392)
ComponentsProtein prgH
KeywordsMEMBRANE PROTEIN / Type III secretion system / inner membrane protein / Cell membrane / Membrane / Transmembrane / Virulence
Function / homology
Function and homology information


GMP Synthetase; Chain A, domain 3 - #170 / Alpha-Beta Plaits - #1780 / Alpha-Beta Plaits - #1770 / Type III secretion system, PrgH/EprH / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / GMP Synthetase; Chain A, domain 3 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYip, C.K. / Vockovic, M. / Yu, A.C. / Strynadka, N.C.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system.
Authors: Spreter, T. / Yip, C.K. / Sanowar, S. / Andre, I. / Kimbrough, T.G. / Vuckovic, M. / Pfuetzner, R.A. / Deng, W. / Yu, A.C. / Finlay, B.B. / Baker, D. / Miller, S.I. / Strynadka, N.C.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Protein prgH
B: Protein prgH
C: Protein prgH
D: Protein prgH
E: Protein prgH
F: Protein prgH
G: Protein prgH
H: Protein prgH


Theoretical massNumber of molelcules
Total (without water)211,7848
Polymers211,7848
Non-polymers00
Water0
1
A: Protein prgH

A: Protein prgH

B: Protein prgH
C: Protein prgH
D: Protein prgH

B: Protein prgH
C: Protein prgH
D: Protein prgH


Theoretical massNumber of molelcules
Total (without water)211,7848
Polymers211,7848
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation4_655x+1,-y,-z1
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area21440 Å2
ΔGint-73 kcal/mol
Surface area75870 Å2
MethodPISA
2
F: Protein prgH

F: Protein prgH

H: Protein prgH

H: Protein prgH

E: Protein prgH
G: Protein prgH

E: Protein prgH
G: Protein prgH


Theoretical massNumber of molelcules
Total (without water)211,7848
Polymers211,7848
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation5_545x+1/2,y-1/2,z1
crystal symmetry operation7_445-x-1/2,y-1/2,-z+1/21
crystal symmetry operation5_445x-1/2,y-1/2,z1
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area22040 Å2
ΔGint-72 kcal/mol
Surface area74160 Å2
MethodPISA
3
A: Protein prgH


Theoretical massNumber of molelcules
Total (without water)26,4731
Polymers26,4731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Protein prgH


Theoretical massNumber of molelcules
Total (without water)26,4731
Polymers26,4731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: Protein prgH


Theoretical massNumber of molelcules
Total (without water)26,4731
Polymers26,4731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: Protein prgH


Theoretical massNumber of molelcules
Total (without water)26,4731
Polymers26,4731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
E: Protein prgH


Theoretical massNumber of molelcules
Total (without water)26,4731
Polymers26,4731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
F: Protein prgH


Theoretical massNumber of molelcules
Total (without water)26,4731
Polymers26,4731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
G: Protein prgH


Theoretical massNumber of molelcules
Total (without water)26,4731
Polymers26,4731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
H: Protein prgH


Theoretical massNumber of molelcules
Total (without water)26,4731
Polymers26,4731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.607, 188.748, 305.563
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
Protein prgH


Mass: 26472.988 Da / Num. of mol.: 8 / Fragment: PrgH periplasmic domain (170-392)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: prgH, STM2874 / Production host: Escherichia coli (E. coli) / References: UniProt: P41783

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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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 16% (w/v) PEG 3350 + 0.2 M tri-ammonium citrate + 0.1M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→152.5 Å / Num. obs: 55188 / % possible obs: 96.5 %

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GR0

3gr0


Resolution: 2.8→152.5 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.873 / SU ML: 0.326 / ESU R: 1.843 / ESU R Free: 0.417
RfactorNum. reflection% reflection
Rfree0.295 2812 5.1 %
Rwork0.247 --
obs-55188 96.5 %
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2--3.11 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.8→152.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12624 0 0 0 12624

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