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- PDB-1a8l: PROTEIN DISULFIDE OXIDOREDUCTASE FROM ARCHAEON PYROCOCCUS FURIOSUS -

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Basic information

Entry
Database: PDB / ID: 1a8l
TitlePROTEIN DISULFIDE OXIDOREDUCTASE FROM ARCHAEON PYROCOCCUS FURIOSUS
ComponentsPROTEIN DISULFIDE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / PDI / THIOREDOXIN FOLD
Function / homology
Function and homology information


Glutaredoxin-like, bacteria/archaea / Thioredoxin domain / Thioredoxin-like domain / Thioredoxin-like fold / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutaredoxin-like protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.9 Å
AuthorsRen, B. / Tibbelin, G. / Pascale, D. / Rossi, M. / Bartolucci, S. / Ladenstein, R.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: A protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus contains two thioredoxin fold units.
Authors: Ren, B. / Tibbelin, G. / de Pascale, D. / Rossi, M. / Bartolucci, S. / Ladenstein, R.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Erratum. A Protein Disulfide Oxidoreductase from the Archaeon Pyrococcus Furiosus Contains Two Thioredoxin Fold Units
Authors: Ren, B. / Tibbelin, G. / De Pascale, D. / Rossi, M. / Bartolucci, S. / Ladenstein, R.
#2: Journal: J.Struct.Biol. / Year: 1997
Title: Crystallization and Preliminary X-Ray Structure Analysis of a Hyperthermostable Thioltransferase from the Archaeon Pyrococcus Furiosus
Authors: Ren, B. / Tibbelin, G. / Pascale, D. / Rossi, M. / Bartolucci, S. / Ladenstein, R.
History
DepositionMar 26, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8782
Polymers25,8131
Non-polymers651
Water2,504139
1
A: PROTEIN DISULFIDE OXIDOREDUCTASE
hetero molecules

A: PROTEIN DISULFIDE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7564
Polymers51,6252
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area1810 Å2
ΔGint-59 kcal/mol
Surface area19560 Å2
MethodPISA, PQS
2
A: PROTEIN DISULFIDE OXIDOREDUCTASE
hetero molecules

A: PROTEIN DISULFIDE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7564
Polymers51,6252
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area2140 Å2
ΔGint-73 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.291, 110.291, 68.514
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-347-

HOH

21A-424-

HOH

31A-425-

HOH

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Components

#1: Protein PROTEIN DISULFIDE OXIDOREDUCTASE


Mass: 25812.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q51760
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
210 mMTris-HCl1drop
30.01 %sodium azide1drop
425 %mPEG5501reservoir
50.2 Mzinc chloride1reservoir
60.1 Mbis-Tris1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 20703 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 16 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.12 / Net I/σ(I): 27
Reflection shellResolution: 1.9→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 7 / Rsym value: 0.3 / % possible all: 96

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→8 Å / Rfactor Rfree error: 0.0049 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1906 10 %RANDOM
Rwork0.192 ---
obs0.192 19064 97.5 %-
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.731 Å20.35 Å20 Å2
2--0.731 Å20 Å2
3---1.736 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 1 139 1951
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2354 233 10.1 %
Rwork0.1984 2061 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.6
LS refinement shell
*PLUS
Rfactor obs: 0.1984

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