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- PDB-7xw1: The crystal structure of AhpD from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 7xw1
TitleThe crystal structure of AhpD from Pseudomonas aeruginosa
ComponentsCarboxymuconolactone decarboxylase family protein
KeywordsOXIDOREDUCTASE / AhpD
Function / homologyperoxiredoxin / Alkylhydroperoxidase AhpD core / Carboxymuconolactone decarboxylase-like / Carboxymuconolactone decarboxylase family / AhpD-like / peroxiredoxin activity / Alkyl hydroperoxide reductase AhpD
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsXu, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The crystal structure of AhpD from Pseudomonas aeruginosa
Authors: Xu, B.
History
DepositionMay 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxymuconolactone decarboxylase family protein


Theoretical massNumber of molelcules
Total (without water)16,2471
Polymers16,2471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.976, 92.976, 65.957
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Carboxymuconolactone decarboxylase family protein / Alkyl hydroperoxide reductase / AhpD


Mass: 16246.528 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U2XNT2
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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M Sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.36→19.88 Å / Num. obs: 7200 / % possible obs: 98.4 % / Redundancy: 19.8 % / Biso Wilson estimate: 55.63 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.062 / Rrim(I) all: 0.277 / Net I/σ(I): 7.8 / Num. measured all: 142387
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.36-2.4511.62.95375716520.310.8543.0820.986.5
8.84-19.8815.60.20125441630.9740.0520.20814.491.5

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O4D

2o4d


Resolution: 2.36→19.88 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3127 719 10.01 %
Rwork0.2489 6465 -
obs0.2552 7184 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.07 Å2 / Biso mean: 67.1866 Å2 / Biso min: 29.81 Å2
Refinement stepCycle: final / Resolution: 2.36→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms999 0 0 0 999
Num. residues----133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.36-2.540.38921300.321177130793
2.54-2.80.38241420.316112801422100
2.8-3.20.41441440.301812861430100
3.2-4.030.33371460.239813181464100
4.03-19.880.24741570.21914041561100

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