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- PDB-3gr5: Periplasmic domain of the outer membrane secretin EscC from enter... -

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Basic information

Entry
Database: PDB / ID: 3gr5
TitlePeriplasmic domain of the outer membrane secretin EscC from enteropathogenic E.coli (EPEC)
ComponentsEscC
KeywordsMEMBRANE PROTEIN / secretin / Type III secretion system / outer membrane / Transport
Function / homology
Function and homology information


type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / cell outer membrane
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #120 / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like ...Ribosomal Protein S8; Chain: A, domain 1 - #120 / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein / 3-Layer(bab) Sandwich / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type 3 secretion system secretin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsYip, C.K. / Vockovic, M. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EscC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1454
Polymers17,8571
Non-polymers2883
Water1,38777
1
A: EscC
hetero molecules

A: EscC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2918
Polymers35,7152
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3320 Å2
ΔGint-73 kcal/mol
Surface area15520 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.645, 90.645, 133.422
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

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Components

#1: Protein EscC


Mass: 17857.307 Da / Num. of mol.: 1 / Fragment: EscC periplasmic domain, residues 21-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: escC / Production host: Escherichia coli (E. coli) / References: UniProt: O52135
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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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: 4.43 Å3/Da / Density % sol: 72.24 %
Crystal growDetails: microbatch, 2.0 M Ammonium sulfate + 0.1 M sodium acetate pH 4.5 or Bis-Tris pH 6.5

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.05→18.7 Å / Num. obs: 20942 / % possible obs: 100 %

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.05→18.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.57 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1072 5.1 %RANDOM
Rwork0.213 ---
obs0.215 20941 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 104.46 Å2 / Biso mean: 42.164 Å2 / Biso min: 19.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.11 Å20 Å2
2---0.23 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.05→18.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 15 77 1329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0221272
X-RAY DIFFRACTIONr_bond_other_d0.0020.021144
X-RAY DIFFRACTIONr_angle_refined_deg2.1021.9841722
X-RAY DIFFRACTIONr_angle_other_deg0.98332686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5765152
X-RAY DIFFRACTIONr_chiral_restr0.1420.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021353
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02239
X-RAY DIFFRACTIONr_nbd_refined0.2310.2279
X-RAY DIFFRACTIONr_nbd_other0.2510.21310
X-RAY DIFFRACTIONr_nbtor_other0.0920.2722
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3140.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.24
X-RAY DIFFRACTIONr_mcbond_it1.7631.5767
X-RAY DIFFRACTIONr_mcangle_it3.24221259
X-RAY DIFFRACTIONr_scbond_it4.3553505
X-RAY DIFFRACTIONr_scangle_it7.1984.5463
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.286 88
Rwork0.248 1433
all-1521

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