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- PDB-2xhf: Crystal structure of peroxiredoxin 5 from Alvinella pompejana -

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Basic information

Entry
Database: PDB / ID: 2xhf
TitleCrystal structure of peroxiredoxin 5 from Alvinella pompejana
ComponentsPEROXIREDOXIN 5
KeywordsOXIDOREDUCTASE / ANTIOXIDANT ENZYMES
Function / homology
Function and homology information


peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / mitochondrion
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesALVINELLA POMPEJANA (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSmeets, A. / Declercq, J.P.
CitationJournal: To be Published
Title: Crystal Structure of Peroxiredoxin 5 from Alvinella Pompejana
Authors: Smeets, A. / Knoops, B. / Declercq, J.P.
History
DepositionJun 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: DEPOSITOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEROXIREDOXIN 5
B: PEROXIREDOXIN 5


Theoretical massNumber of molelcules
Total (without water)38,5362
Polymers38,5362
Non-polymers00
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-11.9 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.540, 92.920, 49.340
Angle α, β, γ (deg.)90.00, 109.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.97091, 0.04785, -0.23461), (0.05463, -0.99825, 0.02246), (-0.23313, -0.03462, -0.97183)
Vector: 2.62997, 106.67894, 45.4888)

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Components

#1: Protein PEROXIREDOXIN 5


Mass: 19268.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ALVINELLA POMPEJANA (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: G1K3P1*PLUS, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS INDICATE THE FOLLOWING MUTATIONS C57S, C82S, C91S, C186S. HOWEVER, AS THERE IS NO ...THE AUTHORS INDICATE THE FOLLOWING MUTATIONS C57S, C82S, C91S, C186S. HOWEVER, AS THERE IS NO UNIPROT SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN, NO SEQADV RECORDS CAN BE ADDED. THE WILD-TYPE SEQUENCE FOR THIS PROTEIN BEGINS AT RESIDUE 37.

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROP RESERVOIR: PEG 14000 17%(W/V), DTT 0.001M, MES PH 6.5 0.1M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.03317
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 9, 2009 / Details: MIRROR 2 VERTICALLY FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL SI(111), HORIZONTALLY FOCUSSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.3→22.2 Å / Num. obs: 81682 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 1.3→1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HD2

1hd2


Resolution: 1.3→22.182 Å / SU ML: 0.14 / σ(F): 1.99 / Phase error: 18.73 / Stereochemistry target values: ML / Details: ANISOTROPIC REFINEMENT OF PROTEIN CHAINS
RfactorNum. reflection% reflection
Rfree0.1841 4126 5.1 %
Rwork0.15 --
obs0.1517 81682 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.351 Å2 / ksol: 0.439 e/Å3
Displacement parametersBiso mean: 22.14 Å2
Baniso -1Baniso -2Baniso -3
1-4.2871 Å20 Å2-2.0471 Å2
2---2.4614 Å20 Å2
3----1.8257 Å2
Refinement stepCycle: LAST / Resolution: 1.3→22.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 0 382 2814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012486
X-RAY DIFFRACTIONf_angle_d1.273362
X-RAY DIFFRACTIONf_dihedral_angle_d11.547931
X-RAY DIFFRACTIONf_chiral_restr0.083373
X-RAY DIFFRACTIONf_plane_restr0.007435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.34650.27724120.21097719X-RAY DIFFRACTION99
1.3465-1.40040.25324250.18877738X-RAY DIFFRACTION100
1.4004-1.46410.22633960.15997781X-RAY DIFFRACTION99
1.4641-1.54130.21044140.14847731X-RAY DIFFRACTION100
1.5413-1.63780.18144140.13237785X-RAY DIFFRACTION100
1.6378-1.76420.18814530.13257710X-RAY DIFFRACTION100
1.7642-1.94170.17443900.13057762X-RAY DIFFRACTION99
1.9417-2.22240.16773970.13087741X-RAY DIFFRACTION99
2.2224-2.79910.17993950.14547729X-RAY DIFFRACTION98
2.7991-22.18470.17234300.15767860X-RAY DIFFRACTION100

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