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

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Basic information

Entry
Database: PDB / ID: 2ayt
TitleThe crystal structure of a protein disulfide oxidoreductase from aquifex aeolicus
Componentsglutaredoxin-like protein
KeywordsOXIDOREDUCTASE / Protein disulfide oxidoreductase / glutaredoxin / thioredoxin fold
Function / homologyGlutaredoxin-like, bacteria/archaea / Thioredoxin domain / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Glutaredoxin-like protein
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPedone, E. / D'Ambrosio, K. / De Simone, G. / Rossi, M. / Pedone, C. / Bartolucci, S.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Insights on a new PDI-like family: structural and functional analysis of a protein disulfide oxidoreductase from the bacterium Aquifex aeolicus
Authors: Pedone, E. / D'Ambrosio, K. / De Simone, G. / Rossi, M. / Pedone, C. / Bartolucci, S.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Crystallization and preliminary X-ray diffraction studies of a protein disulfide oxidoreductase from Aquifex aeolicus
Authors: D'Ambrosio, K. / De Simone, G. / Pedone, E. / Rossi, M. / Bartolucci, S. / Pedone, C.
History
DepositionSep 8, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glutaredoxin-like protein
B: glutaredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0348
Polymers53,4732
Non-polymers5616
Water5,296294
1
A: glutaredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2056
Polymers26,7371
Non-polymers4685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glutaredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8292
Polymers26,7371
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: glutaredoxin-like protein
B: glutaredoxin-like protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)324,20348
Polymers320,84012
Non-polymers3,36336
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area38230 Å2
ΔGint-302 kcal/mol
Surface area105450 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)161.1, 161.1, 153.1
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a monomer

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Components

#1: Protein glutaredoxin-like protein / PROTEIN DISULFIDE OXIDOREDUCTASE


Mass: 26736.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O66753
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, sodium chloride, HEPES, pH 7.5, 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 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 19, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 29372 / Num. obs: 29372 / % possible obs: 98.3 % / Redundancy: 3.6 % / Rsym value: 0.077 / Net I/σ(I): 13.9
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.365 / % possible all: 88.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A8L

1a8l


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1358 -RANDOM
Rwork0.179 ---
obs-27916 93.3 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3623 0 34 294 3951
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.24

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