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- PDB-6jfw: Crystal structure of PA0833 periplasmic domain from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 6jfw
TitleCrystal structure of PA0833 periplasmic domain from Pseudomonas aeruginosa reveals an unexpected enlarged peptidoglycan binding pocket
ComponentsPA0833-PD protein
KeywordsMEMBRANE PROTEIN / Pseudomonas aeruginosa / OmpA C-like protein / PA0833 / PGN-binding basis
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Glycine zipper domain / Glycine zipper / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
OmpA-like domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsLin, X. / Ye, F. / Lin, S. / Yang, F.L. / Chen, Z.M. / Cao, Y. / Chen, Z.J. / Gu, J. / Lu, G.W.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystal structure of PA0833 periplasmic domain from Pseudomonas aeruginosa reveals an unexpected enlarged peptidoglycan binding pocket.
Authors: Lin, X. / Ye, F. / Lin, S. / Yang, F. / Chen, Z. / Cao, Y. / Chen, Z. / Gu, J. / Lu, G.
History
DepositionFeb 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PA0833-PD protein
B: PA0833-PD protein
C: PA0833-PD protein
D: PA0833-PD protein


Theoretical massNumber of molelcules
Total (without water)69,9964
Polymers69,9964
Non-polymers00
Water5,026279
1
A: PA0833-PD protein


Theoretical massNumber of molelcules
Total (without water)17,4991
Polymers17,4991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PA0833-PD protein


Theoretical massNumber of molelcules
Total (without water)17,4991
Polymers17,4991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PA0833-PD protein


Theoretical massNumber of molelcules
Total (without water)17,4991
Polymers17,4991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PA0833-PD protein


Theoretical massNumber of molelcules
Total (without water)17,4991
Polymers17,4991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.436, 47.727, 99.691
Angle α, β, γ (deg.)89.98, 90.03, 90.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PA0833-PD protein


Mass: 17499.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0833
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9I5A7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 1.93 Å3/Da / Density % sol: 36.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate, 0.1M Sodium acetate (pH 4.6), 25% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34416 / % possible obs: 97.8 % / Redundancy: 3.9 % / Rsym value: 0.105 / Net I/σ(I): 13.043
Reflection shellResolution: 2→2.07 Å / Rsym value: 0.414

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2K1S

2k1s


Resolution: 2.002→28.436 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 21.58
RfactorNum. reflection% reflection
Rfree0.2289 1666 4.86 %
Rwork0.1902 --
obs0.1919 34284 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→28.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4308 0 0 279 4587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054364
X-RAY DIFFRACTIONf_angle_d0.7725900
X-RAY DIFFRACTIONf_dihedral_angle_d17.5492696
X-RAY DIFFRACTIONf_chiral_restr0.048644
X-RAY DIFFRACTIONf_plane_restr0.005820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0021-2.0610.2531520.20282535X-RAY DIFFRACTION92
2.061-2.12750.25291160.19332732X-RAY DIFFRACTION97
2.1275-2.20350.28371510.19862693X-RAY DIFFRACTION96
2.2035-2.29170.24511410.20152703X-RAY DIFFRACTION99
2.2917-2.39590.26981740.19632693X-RAY DIFFRACTION96
2.3959-2.52220.25541200.19372801X-RAY DIFFRACTION99
2.5222-2.68010.22021390.20812690X-RAY DIFFRACTION97
2.6801-2.88680.21941390.21212746X-RAY DIFFRACTION98
2.8868-3.1770.2741040.19982829X-RAY DIFFRACTION99
3.177-3.63590.21651700.18512706X-RAY DIFFRACTION99
3.6359-4.57780.19781260.17052801X-RAY DIFFRACTION99
4.5778-28.43880.20091340.17932689X-RAY DIFFRACTION96

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