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- PDB-7y4r: Structure of RclX -

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Basic information

Entry
Database: PDB / ID: 7y4r
TitleStructure of RclX
ComponentsCMD domain-containing protein
KeywordsUNKNOWN FUNCTION / peroxiredoxins / detoxification
Function / homology
Function and homology information


peroxiredoxin activity / oxidoreductase activity
Similarity search - Function
Alkylhydroperoxidase AhpD core / AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
LYSINE / HYDROGEN PEROXIDE / Carboxymuconolactone decarboxylase-like domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsKi, N. / Ha, N.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the putative HOCl and HOSCN-responsive peroxiredoxin RclX from Pseudomonas aeruginosa
Authors: Ki, N. / Ha, N.C.
History
DepositionJun 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: 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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CMD domain-containing protein
B: CMD domain-containing protein
C: CMD domain-containing protein
D: CMD domain-containing protein
E: CMD domain-containing protein
F: CMD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,09913
Polymers70,6356
Non-polymers4647
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27950 Å2
ΔGint-261 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.170, 92.710, 96.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CMD domain-containing protein


Mass: 11772.451 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA0565
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9I5X1
#2: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H2O2
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H15N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate trihydrate pH 4.6 15.5% (v/v) PEG 300

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97942 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 23999 / % possible obs: 96.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 30.01 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.05 / Rrim(I) all: 0.152 / Χ2: 0.993 / Net I/σ(I): 6.5 / Num. measured all: 174870
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.80.3769720.7790.1850.4230.81780.4
2.54-2.593.70.39210790.7350.2040.4450.82287
2.59-2.6440.35711020.8010.1780.4020.83591
2.64-2.694.60.35311370.8340.1620.3910.87293.4
2.69-2.754.80.33511820.8780.1560.3720.86796.6
2.75-2.825.50.33912010.9060.1440.3710.94697.6
2.82-2.896.20.34511870.8980.1390.3740.94197.3
2.89-2.966.60.32611950.9140.1260.3510.97898.9
2.96-3.056.80.3111970.9360.1180.3331.06298.2
3.05-3.157.30.27312110.960.10.2911.04198.9
3.15-3.267.40.26412380.9680.0960.2821.09299
3.26-3.397.80.23912080.9720.0850.2551.13399.2
3.39-3.558.20.20312370.9820.070.2151.13999.4
3.55-3.738.70.17212260.9880.0580.1821.15799.7
3.73-3.978.90.15212280.9870.050.161.15399.7
3.97-4.279.30.12712550.9930.0410.1341.11499.7
4.27-4.790.11512320.9940.0380.1211.04299.7
4.7-5.388.70.10712670.9930.0370.1140.92299.3
5.38-6.7810.50.10112830.9960.0310.1050.82899.7
6.78-5011.40.07413620.9980.0220.0770.77599.2

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DIP

5dip


Resolution: 2.51→37.61 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 2.23 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2665 1103 5.18 %
Rwork0.2065 20175 -
obs0.2095 21278 85.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.09 Å2 / Biso mean: 31.8604 Å2 / Biso min: 5.89 Å2
Refinement stepCycle: final / Resolution: 2.51→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4779 0 28 53 4860
Biso mean--42.2 32.83 -
Num. residues----652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.51-2.620.3217630.24151230129343
2.62-2.760.31781030.23251830193363
2.76-2.930.34911550.23442435259085
2.93-3.160.2621320.21942842297497
3.16-3.470.28631490.21512911306099
3.47-3.980.26221720.192429123084100
3.98-5.010.21621720.181929583130100
5.01-37.610.25161570.20573057321498

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