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- PDB-8hid: HUMAN ERYTHROCYTE CATALSE COMPLEXED WITH BT-Br -

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Basic information

Entry
Database: PDB / ID: 8hid
TitleHUMAN ERYTHROCYTE CATALSE COMPLEXED WITH BT-Br
ComponentsCatalase
KeywordsCYTOSOLIC PROTEIN/INHIBITOR / CYTOSOLIC PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to L-ascorbic acid / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to light intensity ...response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to L-ascorbic acid / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / response to light intensity / catalase / UV protection / response to fatty acid / response to vitamin A / catalase activity / peroxisomal membrane / ureteric bud development / triglyceride metabolic process / Detoxification of Reactive Oxygen Species / antioxidant activity / peroxisomal matrix / positive regulation of cell division / response to vitamin E / response to hyperoxia / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / aerobic respiration / cholesterol metabolic process / response to activity / response to reactive oxygen species / hydrogen peroxide catabolic process / Peroxisomal protein import / response to lead ion / response to insulin / response to hydrogen peroxide / cellular response to growth factor stimulus / osteoblast differentiation / peroxisome / response to estradiol / NADP binding / secretory granule lumen / response to ethanol / ficolin-1-rich granule lumen / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia / response to xenobiotic stimulus / intracellular membrane-bounded organelle / focal adhesion / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain ...Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-LLR / Catalase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLin, H.-Y. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Redox Biol / Year: 2023
Title: A catalase inhibitor: Targeting the NADPH-binding site for castration-resistant prostate cancer therapy.
Authors: Cao, Y.Y. / Chen, Y.Y. / Wang, M.S. / Tong, J.J. / Xu, M. / Zhao, C. / Lin, H.Y. / Mei, L.C. / Dong, J. / Zhang, W.L. / Qin, Y.X. / Huang, W. / Zhang, D. / Yang, G.F.
History
DepositionNov 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catalase
B: Catalase
C: Catalase
D: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,14712
Polymers239,3484
Non-polymers3,7998
Water32,3551796
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48590 Å2
ΔGint-293 kcal/mol
Surface area59010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.466, 140.871, 233.428
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Catalase


Mass: 59836.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAT
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P04040, catalase
#2: Chemical
ChemComp-LLR / (~{S})-azanyl-[2-[[3-bromanyl-4-(diethylamino)phenyl]methyl]hydrazinyl]methanethiol


Mass: 333.291 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H21BrN4S
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1796 / 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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH6.8, 7% PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→39.57 Å / Num. obs: 139142 / % possible obs: 98.6 % / Redundancy: 6.4 % / CC1/2: 0.997 / Net I/σ(I): 15.8
Reflection shellResolution: 2.2→2.22 Å / Num. unique obs: 4286 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dgh

1dgh


Resolution: 2.2→39.57 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 6958 5 %
Rwork0.2249 --
obs0.2269 139142 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15994 0 244 1796 18034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316742
X-RAY DIFFRACTIONf_angle_d0.61522807
X-RAY DIFFRACTIONf_dihedral_angle_d17.5586115
X-RAY DIFFRACTIONf_chiral_restr0.0442305
X-RAY DIFFRACTIONf_plane_restr0.0043040
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.40892260.36684286X-RAY DIFFRACTION99
2.23-2.250.42142260.36044299X-RAY DIFFRACTION98
2.25-2.280.34192290.32384356X-RAY DIFFRACTION99
2.28-2.310.34742280.30224331X-RAY DIFFRACTION99
2.31-2.340.31082280.27264334X-RAY DIFFRACTION99
2.34-2.370.30842300.27054363X-RAY DIFFRACTION99
2.37-2.40.29112290.26714344X-RAY DIFFRACTION99
2.4-2.440.29922300.27384376X-RAY DIFFRACTION100
2.44-2.480.30642290.27144346X-RAY DIFFRACTION99
2.48-2.520.30792310.26684385X-RAY DIFFRACTION99
2.52-2.560.30982280.26694334X-RAY DIFFRACTION99
2.56-2.610.31382300.26064384X-RAY DIFFRACTION99
2.61-2.660.27552300.25644360X-RAY DIFFRACTION100
2.66-2.710.2712290.25534355X-RAY DIFFRACTION99
2.71-2.770.28582330.24274426X-RAY DIFFRACTION100
2.77-2.840.27842290.24394351X-RAY DIFFRACTION99
2.84-2.910.29612310.24854390X-RAY DIFFRACTION99
2.91-2.990.30782330.24654427X-RAY DIFFRACTION99
2.99-3.070.27452310.23344393X-RAY DIFFRACTION100
3.07-3.170.26312320.22634397X-RAY DIFFRACTION100
3.17-3.290.28162320.22254407X-RAY DIFFRACTION100
3.29-3.420.2742340.21714444X-RAY DIFFRACTION100
3.42-3.570.24092320.21434412X-RAY DIFFRACTION100
3.57-3.760.24582350.20644461X-RAY DIFFRACTION100
3.76-40.23482350.19134468X-RAY DIFFRACTION100
4-4.30.21182350.18594459X-RAY DIFFRACTION100
4.3-4.740.23892350.17884483X-RAY DIFFRACTION100
4.74-5.420.21632380.18094523X-RAY DIFFRACTION100
5.42-6.820.23132410.18724567X-RAY DIFFRACTION100
6.82-39.570.21372490.18444723X-RAY DIFFRACTION99

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