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- PDB-4gqf: Aeropyrum pernix Peroxiredoxin Q Enzyme in the Locally Unfolded C... -

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Basic information

Entry
Database: PDB / ID: 4gqf
TitleAeropyrum pernix Peroxiredoxin Q Enzyme in the Locally Unfolded Conformation
ComponentsThiol peroxidase
KeywordsOXIDOREDUCTASE / peroxiredoxin / dimer / PrxQ / BCP / locally-unfolded / CxxxxC / reduces peroxides / disulfide
Function / homology
Function and homology information


peroxidase activity
Similarity search - Function
Peroxiredoxin, AhpC-type / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPerkins, A. / Karplus, P.A. / Gretes, M.C. / Nelson, K.J. / Poole, L.B.
CitationJournal: Biochemistry / Year: 2012
Title: Mapping the Active Site Helix-to-Strand Conversion of CxxxxC Peroxiredoxin Q Enzymes.
Authors: Perkins, A. / Gretes, M.C. / Nelson, K.J. / Poole, L.B. / Karplus, P.A.
History
DepositionAug 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 0THIS ENTRY 4GQF REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2CX3SF) ...THIS ENTRY 4GQF REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2CX3SF) DETERMINED BY AUTHORS OF THE PDB ENTRY 2CX3: E.MIZOHATA, K.MURAYAMA, M.IDAKA, A.TATSUGUCHI, T.TERADA, M.SHIROUZU, S.YOKOYAMA, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol peroxidase
B: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,71913
Polymers37,6712
Non-polymers1,04911
Water1,22568
1
A: Thiol peroxidase
hetero molecules

A: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,43110
Polymers37,6712
Non-polymers7618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area3530 Å2
ΔGint-70 kcal/mol
Surface area15030 Å2
MethodPISA
2
B: Thiol peroxidase
hetero molecules

B: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,00816
Polymers37,6712
Non-polymers1,33714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-2/31
Buried area4570 Å2
ΔGint-150 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.000, 127.000, 104.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11B-206-

SO4

21B-207-

SO4

31A-1022-

HOH

41B-328-

HOH

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Components

#1: Protein Thiol peroxidase / Peroxiredoxin Q


Mass: 18835.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea)
Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
Gene: APE2125, APE_2125.1, bcp / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9YA14, peroxiredoxin
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.04 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2CX3.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CX3

2cx3


Resolution: 2.3→25.42 Å / Cor.coef. Fo:Fc: 0.9627 / Cor.coef. Fo:Fc free: 0.9545 / Occupancy max: 1 / Occupancy min: 0.25 / SU R Cruickshank DPI: 0.204 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.208 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 1162 5.12 %RANDOM
Rwork0.186 ---
obs0.1879 22682 99.97 %-
Displacement parametersBiso max: 198.9 Å2 / Biso mean: 80.1562 Å2 / Biso min: 36.64 Å2
Baniso -1Baniso -2Baniso -3
1--3.5498 Å20 Å20 Å2
2---3.5498 Å20 Å2
3---7.0995 Å2
Refine analyzeLuzzati coordinate error obs: 0.486 Å
Refinement stepCycle: LAST / Resolution: 2.3→25.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 57 68 2705
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d918SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes375HARMONIC5
X-RAY DIFFRACTIONt_it2695HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion333SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3072SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2695HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3664HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion19.06
LS refinement shellResolution: 2.3→2.41 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2771 138 4.68 %
Rwork0.2616 2808 -
all0.2623 2946 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.14712.4545-0.53064.431-0.09790.99420.436-0.35290.45640.6984-0.25360.3753-0.19380.0082-0.18250.4545-0.27390.0928-0.1559-0.0688-0.1066-59.792815.2803-18.894
21.67161.21850.73183.823-0.04571.487-0.13830.2233-0.4416-0.03760.1366-0.53560.35790.3120.00170.2673-0.18490.0755-0.0894-0.1248-0.001-41.02616.3284-39.6999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|164 }A2 - 164
2X-RAY DIFFRACTION2{ B|3 - B|164 }B3 - 164

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