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- PDB-1dgf: HUMAN ERYTHROCYTE CATALASE -

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Basic information

Entry
Database: PDB / ID: 1dgf
TitleHUMAN ERYTHROCYTE CATALASE
ComponentsCATALASE
KeywordsOXIDOREDUCTASE / CATALASE / HEME / NADPH / HYDROGEN PEROXIDE
Function / homology
Function and homology information


response to amitrole / response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / catalase ...response to amitrole / response to phenylpropanoid / aminoacylase activity / catalase complex / hemoglobin metabolic process / response to inactivity / cellular detoxification of hydrogen peroxide / response to ozone / oxidoreductase activity, acting on peroxide as acceptor / catalase / response to L-ascorbic acid / response to fatty acid / UV protection / response to light intensity / catalase activity / response to vitamin A / peroxisomal membrane / ureteric bud development / triglyceride metabolic process / response to vitamin E / Detoxification of Reactive Oxygen Species / antioxidant activity / peroxisomal matrix / positive regulation of cell division / response to hyperoxia / Mitochondrial unfolded protein response (UPRmt) / response to cadmium ion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cholesterol metabolic process / aerobic respiration / response to reactive oxygen species / response to activity / hydrogen peroxide catabolic process / Peroxisomal protein import / response to hydrogen peroxide / response to insulin / cellular response to growth factor stimulus / response to lead ion / osteoblast differentiation / peroxisome / response to estradiol / NADP binding / response to ethanol / secretory granule lumen / ficolin-1-rich granule lumen / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to xenobiotic stimulus / focal adhesion / intracellular membrane-bounded organelle / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / extracellular region / metal ion binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Catalase, clade 3 / Cytochrome C Oxidase; Chain J / Catalase, mono-functional, haem-containing, clades 1 and 3 / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. ...Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Catalase, clade 3 / Cytochrome C Oxidase; Chain J / Catalase, mono-functional, haem-containing, clades 1 and 3 / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Few Secondary Structures / Irregular / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / Catalase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsPutnam, C.D. / Arvai, A.S. / Bourne, Y. / Tainer, J.A.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Active and inhibited human catalase structures: ligand and NADPH binding and catalytic mechanism.
Authors: Putnam, C.D. / Arvai, A.S. / Bourne, Y. / Tainer, J.A.
History
DepositionNov 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)230,69814
Polymers226,5054
Non-polymers4,19310
Water41,4162299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52030 Å2
ΔGint-300 kcal/mol
Surface area57890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.717, 142.505, 232.066
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CATALASE


Mass: 56626.359 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: ERYTHROCYTE / References: UniProt: P04040, catalase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2299 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 6.5 - 8.0% PEG4000, PROTEIN AT 40 MG/ML IN 50MM TRISCL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
250 mMTris-HCl1drop
36.5-8.0 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 401102 / Num. obs: 401102 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 14.2 Å2 / Rsym value: 0.045 / Net I/σ(I): 20
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.8 % / Rsym value: 0.279 / % possible all: 82.2
Reflection
*PLUS
Num. measured all: 1131638 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 82.2 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: Bond Angles and Lengths to the Heme Iron from both the TYR358 ligand and the Heme Nitrogens were unconstrained
RfactorNum. reflectionSelection details
Rfree0.192 40217 RANDOM, 10%
Rwork0.172 --
all0.174 400233 -
obs0.174 400233 -
Displacement parametersBiso mean: 15.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.1111 Å20 Å20 Å2
2---0.6715 Å20 Å2
3----1.4396 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16092 0 284 2299 18675
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_mcbond_it2.2421.5
X-RAY DIFFRACTIONx_mcangle_it2.3172
X-RAY DIFFRACTIONx_scbond_it2.7982
X-RAY DIFFRACTIONx_scangle_it2.7822.5
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d

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