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- PDB-1prx: HORF6 A NOVEL HUMAN PEROXIDASE ENZYME -

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Basic information

Entry
Database: PDB / ID: 1prx
TitleHORF6 A NOVEL HUMAN PEROXIDASE ENZYME
ComponentsHORF6
KeywordsANTIOXIDANT / PEROXIREDOXIN / HORF6 / HYDROGEN PEROXIDE / REDOX REGULATION / CELLULAR SIGNALING
Function / homology
Function and homology information


1-acylglycerophosphocholine O-acyltransferase / 1-acylglycerophosphocholine O-acyltransferase activity / glycerophospholipid catabolic process / glutathione-dependent peroxiredoxin / calcium-independent phospholipase A2 activity / phospholipase A2 activity / peroxiredoxin activity / glutathione peroxidase activity / positive regulation of mRNA splicing, via spliceosome / phospholipase A2 ...1-acylglycerophosphocholine O-acyltransferase / 1-acylglycerophosphocholine O-acyltransferase activity / glycerophospholipid catabolic process / glutathione-dependent peroxiredoxin / calcium-independent phospholipase A2 activity / phospholipase A2 activity / peroxiredoxin activity / glutathione peroxidase activity / positive regulation of mRNA splicing, via spliceosome / phospholipase A2 / cellular oxidant detoxification / Detoxification of Reactive Oxygen Species / cell redox homeostasis / hydrogen peroxide catabolic process / peroxidase activity / azurophil granule lumen / response to oxidative stress / cadherin binding / ubiquitin protein ligase binding / Neutrophil degranulation / perinuclear region of cytoplasm / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / 1-Cys peroxiredoxin / Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain ...Antioxidant, Horf6; Chain A, domain 2 / Antioxidant, Horf6; Chain A, domain2 / 1-Cys peroxiredoxin / Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsChoi, H.-J. / Kang, S.W. / Yang, C.-H. / Rhee, S.G. / Ryu, S.-E.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of a novel human peroxidase enzyme at 2.0 A resolution.
Authors: Choi, H.J. / Kang, S.W. / Yang, C.H. / Rhee, S.G. / Ryu, S.E.
History
DepositionApr 3, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: HORF6
B: HORF6


Theoretical massNumber of molelcules
Total (without water)50,1362
Polymers50,1362
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-40 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.850, 75.170, 63.300
Angle α, β, γ (deg.)90.00, 110.21, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99988, -0.01523, 0.00341), (-0.0154, 0.92706, -0.37459), (0.00255, -0.3746, -0.92718)
Vector: 55.74726, 7.07527, 34.79962)

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Components

#1: Protein HORF6


Mass: 25067.904 Da / Num. of mol.: 2 / Mutation: C91S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P30041
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 8

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %(w/v)PEG40001reservoir
20.2 Mmagnesium acetate1reservoir
30.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→8 Å / Num. obs: 24439 / % possible obs: 93.7 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 17
Reflection shellResolution: 2→2.25 Å / Redundancy: 3 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 6.1 / Rsym value: 0.189 / % possible all: 91.4
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å
Reflection shell
*PLUS
% possible obs: 91.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 2→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1287 5 %RANDOM
Rwork0.191 ---
obs0.191 23097 93.7 %-
Displacement parametersBiso mean: 20.91 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 0 0 112 3686
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.525
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.79
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.346
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.25 Å
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.79
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.346

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