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- PDB-4ec5: Crystal structure of the S210C (dimer) mutant from the N-terminal... -

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Basic information

Entry
Database: PDB / ID: 4ec5
TitleCrystal structure of the S210C (dimer) mutant from the N-terminal domain of the secretin XcpQ from Pseudomonas aeruginosa
ComponentsGeneral secretion pathway protein D
KeywordsPROTEIN TRANSPORT / XcpQ / structural protein / N-terminal domain of the secretin / periplasmic space / outer membrane
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / protein secretion / cell outer membrane / identical protein binding
Similarity search - Function
: / GspD-like, N0 domain / Ribosomal Protein S8; Chain: A, domain 1 - #120 / Type II secretion system protein GspD / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily ...: / GspD-like, N0 domain / Ribosomal Protein S8; Chain: A, domain 1 - #120 / Type II secretion system protein GspD / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å
AuthorsVan der Meeren, R. / Savvides, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: New Insights into the Assembly of Bacterial Secretins: STRUCTURAL STUDIES OF THE PERIPLASMIC DOMAIN OF XcpQ FROM PSEUDOMONAS AERUGINOSA.
Authors: Van der Meeren, R. / Wen, Y. / Van Gelder, P. / Tommassen, J. / Devreese, B. / Savvides, S.N.
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Feb 6, 2013Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: General secretion pathway protein D
B: General secretion pathway protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1123
Polymers53,0722
Non-polymers401
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: General secretion pathway protein D


Theoretical massNumber of molelcules
Total (without water)26,5361
Polymers26,5361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: General secretion pathway protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5762
Polymers26,5361
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.790, 39.780, 93.900
Angle α, β, γ (deg.)90.00, 99.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-301-

CA

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Components

#1: Protein General secretion pathway protein D


Mass: 26535.959 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 35-277 / Mutation: S210C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692/PAO1/1C/PRS 101/LMG 12228 / Gene: xcpQ, PA3105 / Production host: Escherichia coli (E. coli) / References: UniProt: P35818
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.09 Å3/Da / Density % sol: 41.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 14% PEG8000, 0.2M Calcium acetate hydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.197→50 Å / Num. all: 22844 / Num. obs: 22248 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
DNAdata collection
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.197→46.602 Å / SU ML: 0.25 / σ(F): 1.99 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1117 5.02 %5% of total reflections, using the Rfree-flag generation in phenix
Rwork0.213 ---
obs0.2141 22245 97.41 %-
all-22844 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.277 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5957 Å2-0 Å21.8794 Å2
2--1.4241 Å20 Å2
3----3.0198 Å2
Refinement stepCycle: LAST / Resolution: 2.197→46.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 1 141 3231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073148
X-RAY DIFFRACTIONf_angle_d1.1654315
X-RAY DIFFRACTIONf_dihedral_angle_d14.1481090
X-RAY DIFFRACTIONf_chiral_restr0.079541
X-RAY DIFFRACTIONf_plane_restr0.004559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.197-2.29740.33631340.26032550X-RAY DIFFRACTION96
2.2974-2.41850.30891390.25382610X-RAY DIFFRACTION97
2.4185-2.570.28071360.23982618X-RAY DIFFRACTION98
2.57-2.76840.27751390.22942667X-RAY DIFFRACTION98
2.7684-3.04690.23711420.22192652X-RAY DIFFRACTION98
3.0469-3.48770.24931380.22292648X-RAY DIFFRACTION98
3.4877-4.39360.18971440.18562668X-RAY DIFFRACTION98
4.3936-46.61210.1891450.1922715X-RAY DIFFRACTION96

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