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- PDB-2hls: The crystal structure of a protein disulfide oxidoreductase from ... -

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Basic information

Entry
Database: PDB / ID: 2hls
TitleThe crystal structure of a protein disulfide oxidoreductase from Aeropyrum pernix k1
Componentsprotein disulfide oxidoreductaseProtein-disulfide reductase
KeywordsOXIDOREDUCTASE / protein disulfide oxidoreductase / thioredoxin fold
Function / homology
Function and homology information


Glutaredoxin-like, bacteria/archaea / Thioredoxin domain / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein-disulfide oxidoreductase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsD'Ambrosio, K. / De Simone, G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: A Novel Member of the Protein Disulfide Oxidoreductase Family from Aeropyrum pernix K1: Structure, Function and Electrostatics.
Authors: D'Ambrosio, K. / Pedone, E. / Langella, E. / De Simone, G. / Rossi, M. / Pedone, C. / Bartolucci, S.
History
DepositionJul 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: protein disulfide oxidoreductase
B: protein disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7994
Polymers54,7282
Non-polymers712
Water7,638424
1
A: protein disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4002
Polymers27,3641
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: protein disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4002
Polymers27,3641
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: protein disulfide oxidoreductase
B: protein disulfide oxidoreductase
hetero molecules

A: protein disulfide oxidoreductase
B: protein disulfide oxidoreductase
hetero molecules

A: protein disulfide oxidoreductase
B: protein disulfide oxidoreductase
hetero molecules

A: protein disulfide oxidoreductase
B: protein disulfide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,19716
Polymers218,9138
Non-polymers2848
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area19380 Å2
ΔGint-147 kcal/mol
Surface area70750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.625, 101.424, 128.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a monomer

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Components

#1: Protein protein disulfide oxidoreductase / Protein-disulfide reductase


Mass: 27364.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): Rb791 / References: UniProt: Q9YDZ4
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2M ammonium sulfate, 2% PEG 400, 0.1M HEPES, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.93→20 Å / Num. obs: 44495 / % possible obs: 98.1 % / Rsym value: 0.034 / Net I/σ(I): 36.9
Reflection shellResolution: 1.93→2 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.297 / % possible all: 87.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2AYT

2ayt


Resolution: 1.93→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.209 2111 RANDOM
Rwork0.187 --
all-44914 -
obs-41970 -
Refinement stepCycle: LAST / Resolution: 1.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 2 424 4084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.005

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