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- PDB-1f4j: STRUCTURE OF TETRAGONAL CRYSTALS OF HUMAN ERYTHROCYTE CATALASE -

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Basic information

Entry
Database: PDB / ID: 1f4j
TitleSTRUCTURE OF TETRAGONAL CRYSTALS OF HUMAN ERYTHROCYTE CATALASE
ComponentsCATALASE
KeywordsOXIDOREDUCTASE / heme protein / no bound NADPH
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 / response to L-ascorbic acid ...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 / response to L-ascorbic acid / catalase / response to fatty acid / UV protection / response to light intensity / response to vitamin A / catalase activity / 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) / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / 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 lead ion / response to insulin / cellular response to growth factor stimulus / osteoblast differentiation / peroxisome / NADP binding / response to estradiol / 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 / cytosol / cytoplasm
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / 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, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsSafo, M.K. / Musayev, F.N. / Wu, S.H. / Abraham, D.J. / Ko, T.P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of tetragonal crystals of human erythrocyte catalase.
Authors: Safo, M.K. / Musayev, F.N. / Wu, S.H. / Abraham, D.J. / Ko, T.P.
History
DepositionJun 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)241,8148
Polymers239,3484
Non-polymers2,4664
Water22,3211239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44100 Å2
ΔGint-277 kcal/mol
Surface area56630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.600, 203.600, 144.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsTetramer of identical subunits A, B, C and D. Assembled with a 222 point-group symmetry

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Components

#1: Protein
CATALASE


Mass: 59836.996 Da / Num. of mol.: 4 / Fragment: INTACT BUT LACKS THE FIRST AND LAST EXONS / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: ERYTHROCYTE / Tissue: BLOOD / References: UniProt: P04040, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 1239 / 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: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: potassium sodium tartrate, HEPES, sodium acetate, potassium chloride, 2-mercaptoethanol, EDTA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 6.7
Details: Ko, T.P., (2000) Acta Crystallogr., Sect.D, 56, 241.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
20.7 Mpotassium sodium tartrate1reservoir
30.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→204 Å / Num. all: 116954 / Num. obs: 107950 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.8
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.249 / Num. unique all: 10206 / % possible all: 76.4
Reflection
*PLUS
Lowest resolution: 144 Å / Num. measured all: 337583
Reflection shell
*PLUS
% possible obs: 76.4 % / Num. unique obs: 10206 / Num. measured obs: 23586 / Mean I/σ(I) obs: 1.66

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
bioteXdata reduction
bioteXdata scaling
RefinementResolution: 2.4→204 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Used noncrystallographic symmetry restraints but released in final cycles of refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 8677 -RANDOM
Rwork0.196 ---
all0.2 107871 --
obs0.2 107871 93.8 %-
Refinement stepCycle: LAST / Resolution: 2.4→204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15402 0 172 1239 16813
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.0083
X-RAY DIFFRACTIONc_bond_d1.45
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.19
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 144 Å / σ(F): 0 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0083
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.19
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / Rfactor Rfree: 0.406 / Rfactor obs: 0.384

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