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- PDB-4gqc: Crystal Structure of Aeropyrum pernix Peroxiredoxin Q Enzyme in F... -

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Basic information

Entry
Database: PDB / ID: 4gqc
TitleCrystal Structure of Aeropyrum pernix Peroxiredoxin Q Enzyme in Fully-Folded and Locally-Unfolded Conformations
ComponentsThiol peroxidase
KeywordsOXIDOREDUCTASE / CXXXXC Motif / fully folded / locally unfolded / peroxide / DTT / Structural Genomics / RIKEN / peroxiredoxin / 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
DITHIANE DIOL / Thiol peroxidase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 4GQC REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2CX4SF) ...THIS ENTRY 4GQC REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2CX4SF) DETERMINED BY AUTHORS OF THE PDB ENTRY 2CX4: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,33740
Polymers74,7784
Non-polymers3,55936
Water4,900272
1
A: Thiol peroxidase
C: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,17120
Polymers37,3892
Non-polymers1,78118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-180 kcal/mol
Surface area14800 Å2
MethodPISA
2
B: Thiol peroxidase
D: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,16720
Polymers37,3892
Non-polymers1,77718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-156 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.388, 132.388, 106.536
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein
Thiol peroxidase / Peroxiredoxin Q


Mass: 18694.604 Da / Num. of mol.: 4
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 3.12 Å3/Da / Density % sol: 60.59 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2CX4.

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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 2CX4

2cx4


Resolution: 2→49.42 Å / Cor.coef. Fo:Fc: 0.9655 / Cor.coef. Fo:Fc free: 0.9499 / Occupancy max: 1 / Occupancy min: 0.2 / SU R Cruickshank DPI: 0.144 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.148 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.139
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 3267 5.1 %RANDOM
Rwork0.1948 ---
obs0.1969 63966 99.49 %-
Displacement parametersBiso max: 185.2 Å2 / Biso mean: 60.9005 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-3.0582 Å20 Å20 Å2
2--3.0582 Å20 Å2
3----6.1163 Å2
Refine analyzeLuzzati coordinate error obs: 0.377 Å
Refinement stepCycle: LAST / Resolution: 2→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5164 0 189 272 5625
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1910SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes756HARMONIC5
X-RAY DIFFRACTIONt_it5515HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion673SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6353SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5515HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7505HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion17.52
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3227 223 5.04 %
Rwork0.2989 4205 -
all0.3001 4428 -
obs--99.49 %
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)
15.23730.8255-0.15253.15220.55210.84350.1334-0.43771.0333-0.1697-0.20.6498-0.1066-0.09540.0666-0.26110.0163-0.0283-0.2385-0.19590.3072-39.209451.0818-7.4718
23.9731.0448-0.30053.1817-0.32460.9467-0.0381-0.3152-0.5699-0.2264-0.1876-0.54420.05350.1660.2258-0.20620.03030.0455-0.15620.13640.1897-27.247914.5965-8.5224
35.68080.9695-1.98222.2701-0.53031.40390.0559-0.2890.6877-0.35520.1074-0.2292-0.21670.1745-0.1633-0.1385-0.04560.1554-0.2332-0.09410.1698-8.432347.8596-15.9338
45.45050.85871.34662.22730.22511.1579-0.0945-0.2951-0.2054-0.43080.0030.6620.0328-0.13110.0915-0.16670.0037-0.1962-0.2606-0.00880.2579-58.342417.9884-15.8448
52.37852.36970.01710.64330.23020.78390.027-0.1630.1111-0.842-0.12590.2307-0.0716-0.11920.09890.06260.14430.0093-0.1421-0.01770.4122-35.936830.8681-11.5893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|4 - A|163 }A4 - 163
2X-RAY DIFFRACTION2{ B|4 - B|163 }B4 - 163
3X-RAY DIFFRACTION3{ C|3 - C|163 }C3 - 163
4X-RAY DIFFRACTION4{ D|3 - D|163 }D3 - 163
5X-RAY DIFFRACTION5{ A|201 - A|210 B|201 - B|210 C|203 - C|208 D|203 - D|208 }A201 - 210
6X-RAY DIFFRACTION5{ A|201 - A|210 B|201 - B|210 C|203 - C|208 D|203 - D|208 }B201 - 210
7X-RAY DIFFRACTION5{ A|201 - A|210 B|201 - B|210 C|203 - C|208 D|203 - D|208 }C203 - 208
8X-RAY DIFFRACTION5{ A|201 - A|210 B|201 - B|210 C|203 - C|208 D|203 - D|208 }D202 - 208

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