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- PDB-4o5p: Crystal structure of an uncharacterized protein from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 4o5p
TitleCrystal structure of an uncharacterized protein from Pseudomonas aeruginosa
ComponentsUncharacterized protein
KeywordsHYDROLASE / phospholipase effector
Function / homology: / T6SS, Phospholipase effector Tle1-like, C-terminal domain / Domain of unknown function DUF2235 / T6SS, Phospholipase effector Tle1-like, catalytic domain / DUF2235 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsHu, H.D. / Gao, Z.Q. / Zhang, H. / Dong, Y.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the type VI secretion phospholipase effector Tle1 provides insight into its hydrolysis and membrane targeting.
Authors: Hu, H.D. / Zhang, H. / Gao, Z.Q. / Wang, D. / Liu, G. / Xu, J. / Lan, K. / Dong, Y.H.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)195,1492
Polymers195,1492
Non-polymers00
Water18,4651025
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)97,5751
Polymers97,5751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)97,5751
Polymers97,5751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.603, 81.078, 92.145
Angle α, β, γ (deg.)97.83, 89.96, 90.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Uncharacterized protein / phospholipase effector


Mass: 97574.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3290 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYV3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1025 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.04M citric acid, 0.1M Bis-Tris propane, 17% pEG 3350 , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 25, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 109609 / Num. obs: 109609 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 24.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.3 / Num. unique all: 5486 / % possible all: 92.3

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Processing

Software
NameVersionClassification
MAR345data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.001→28.298 Å / SU ML: 0.29 / σ(F): 1.96 / Phase error: 28.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 5266 4.97 %random
Rwork0.2258 ---
all0.228 109609 --
obs0.2258 105980 88.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→28.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11509 0 0 1025 12534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811761
X-RAY DIFFRACTIONf_angle_d1.19915910
X-RAY DIFFRACTIONf_dihedral_angle_d15.1154337
X-RAY DIFFRACTIONf_chiral_restr0.0781714
X-RAY DIFFRACTIONf_plane_restr0.0052110
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0011-2.02380.2953230.2354605181
2.0238-2.04760.29093780.2298672189
2.0476-2.07260.29073690.2262674491
2.0726-2.09880.29143160.2245678990
2.0988-2.12640.31393100.241692289
2.1264-2.15550.32833420.2407676792
2.1555-2.18630.36243220.3354672088
2.1863-2.2190.56742790.4579615581
2.219-2.25360.45813560.4181673990
2.2536-2.29050.43390.3553643985
2.2905-2.330.45463610.3945604381
2.33-2.37240.33123520.2406675288
2.3724-2.4180.27293500.2346672390
2.418-2.46730.30293530.2261673789
2.4673-2.52090.28283210.2195676990
2.5209-2.57950.29623870.2276671489
2.5795-2.6440.26223400.229664489
2.644-2.71540.27783190.2219668888
2.7154-2.79530.28843500.2324653086
2.7953-2.88540.31523160.2163654487
2.8854-2.98840.2533940.2316656787
2.9884-3.10790.28054140.2224634386
3.1079-3.24920.24993050.2203666487
3.2492-3.42020.25653950.205665589
3.4202-3.63410.22873580.1988668489
3.6341-3.9140.23833520.1977697392
3.914-4.30670.21183590.1779711394
4.3067-4.9270.19514070.1692741499
4.927-6.19680.233990.1917753299
6.1968-28.3010.20463660.2059729297

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