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- PDB-1aor: STRUCTURE OF A HYPERTHERMOPHILIC TUNGSTOPTERIN ENZYME, ALDEHYDE F... -

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Basic information

Entry
Database: PDB / ID: 1aor
TitleSTRUCTURE OF A HYPERTHERMOPHILIC TUNGSTOPTERIN ENZYME, ALDEHYDE FERREDOXIN OXIDOREDUCTASE
ComponentsALDEHYDE FERREDOXIN OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


aldehyde ferredoxin oxidoreductase / aldehyde ferredoxin oxidoreductase activity / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 3 / Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 3 / Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2 / Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2 / Aldehyde Ferredoxin Oxidoreductase; A, domain 1 / Aldehyde ferredoxin oxidoreductase, N-terminal domain / Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 ...Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 3 / Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 3 / Aldehyde Ferredoxin Oxidoreductase Protein, subunit A; domain 2 / Aldehyde Ferredoxin Oxidoreductase Protein, subunit A, domain 2 / Aldehyde Ferredoxin Oxidoreductase; A, domain 1 / Aldehyde ferredoxin oxidoreductase, N-terminal domain / Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 / Aldehyde ferredoxin oxidoreductase-like, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal domain superfamily / : / Aldehyde ferredoxin oxidoreductase, domains 2 & 3 / Aldehyde ferredoxin oxidoreductase, N-terminal domain / Aldehyde ferredoxin oxidoreductase, N-terminal domain / 4-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / TUNGSTOPTERIN COFACTOR / IRON/SULFUR CLUSTER / Tungsten-containing aldehyde ferredoxin oxidoreductase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsChan, M.K. / Mukund, S. / Kletzin, A. / Adams, M.W.W. / Rees, D.C.
Citation
Journal: Science / Year: 1995
Title: Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase.
Authors: Chan, M.K. / Mukund, S. / Kletzin, A. / Adams, M.W. / Rees, D.C.
#1: Journal: To be Published
Title: Molecular Characterization of the Genes Encoding Two Tungsten-Containing Enzymes from Hyperthermophilic Archaea: Aldehyde Ferredoxin Oxidoreductase from Pyrococcus Furiosus and Formaldehyde ...Title: Molecular Characterization of the Genes Encoding Two Tungsten-Containing Enzymes from Hyperthermophilic Archaea: Aldehyde Ferredoxin Oxidoreductase from Pyrococcus Furiosus and Formaldehyde Ferredoxin Oxidoreductase from Thermococcus Litoralis
Authors: Kletzin, A. / Mukund, S. / Kelley-Crouse, T.L. / Chan, M.K. / Rees, D.C. / Adams, M.W.W.
History
DepositionFeb 13, 1995Processing site: BNL
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET HELIX AND SHEET ENTRIES HAVE BEEN AUTOMATICALLY GENERATED BY THE PDB USING A PROGRAM BASED ON ...SHEET HELIX AND SHEET ENTRIES HAVE BEEN AUTOMATICALLY GENERATED BY THE PDB USING A PROGRAM BASED ON DSSP OF W. KABSCH AND C. SANDER

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALDEHYDE FERREDOXIN OXIDOREDUCTASE
B: ALDEHYDE FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,2999
Polymers133,4302
Non-polymers2,8697
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-101 kcal/mol
Surface area35650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.939, 108.332, 159.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 310 / 2: CIS PROLINE - PRO A 462 / 3: CIS PROLINE - PRO B 310 / 4: CIS PROLINE - PRO B 462

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALDEHYDE FERREDOXIN OXIDOREDUCTASE


Mass: 66715.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / References: UniProt: Q51739

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Non-polymers , 5 types, 386 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-PTE / TUNGSTOPTERIN COFACTOR


Mass: 1031.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29MgN10O14P2S4W
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal grow
*PLUS
pH: 8 / Method: capillary method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein11
250 mMTris-HCl11
310 %glycerol11
42 mMdithionite11
52 mMdithiothreitol11
60.18 M12Na2MoO4
70.1 MTris-HCl12
830 %PEG400012

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 56373 / % possible obs: 92.4 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.32 Å / Num. measured all: 237105 / Rmerge(I) obs: 0.049

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→10 Å / σ(F): 0
Details: PLEASE NOTE THAT ALL RESIDUES WERE BUILT TO FIT THE BEST POSSIBLE OBSERVED DENSITY. THOSE SIDE CHAIN ATOMS WHICH SEEMED UNRELIABLE HAD THEIR OCCUPANCIES FIXED AT 0.0.
RfactorNum. reflection% reflection
Rwork0.155 --
obs0.155 55520 89 %
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9386 0 129 373 9888
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg2.576
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 22 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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