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- PDB-1b4n: FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS, ... -

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Basic information

Entry
Database: PDB / ID: 1b4n
TitleFORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS, COMPLEXED WITH GLUTARATE
ComponentsFORMALDEHYDE FERREDOXIN OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / TUNGSTOENZYME / MOCO / TUNGSTEN CONTAINING PROTEIN / HYPERTHERMOPHILE
Function / homology
Function and homology information


aldehyde ferredoxin oxidoreductase activity / aldehyde ferredoxin oxidoreductase / 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
GLUTARIC ACID / TUNGSTOPTERIN COFACTOR / IRON/SULFUR CLUSTER / aldehyde ferredoxin oxidoreductase / aldehyde ferredoxin oxidoreductase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHu, Y.L. / Faham, S. / Roy, R. / Adams, M.W.W. / Rees, D.C.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus: the 1.85 A resolution crystal structure and its mechanistic implications.
Authors: Hu, Y. / Faham, S. / Roy, R. / Adams, M.W. / Rees, D.C.
#1: Journal: J.Bacteriol. / Year: 1999
Title: Purification and Molecular Characterization of the Tungsten-Containing Formaldehyde Ferredoxin Oxidoreductase from the Hyperthermophilic Archaeon Pyrococcus Furiosus: The Third of a Putative ...Title: Purification and Molecular Characterization of the Tungsten-Containing Formaldehyde Ferredoxin Oxidoreductase from the Hyperthermophilic Archaeon Pyrococcus Furiosus: The Third of a Putative Five-Member Tungstoenzyme Family
Authors: Roy, R. / Mukund, S. / Schut, G.J. / Dunn, D.M. / Weiss, R. / Adams, M.W.
History
DepositionDec 24, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 7, 2011Group: Database references
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE
B: FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE
C: FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE
D: FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,66620
Polymers275,4434
Non-polymers6,22316
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-180 kcal/mol
Surface area71640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.400, 170.500, 180.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99175, -0.10396, -0.07494), (-0.0869, 0.11575, 0.98947), (-0.0942, 0.98782, -0.12383)112.41776, -31.91685, 46.79736
2given(0.81605, 0.46218, -0.34708), (0.4612, -0.88262, -0.09096), (-0.34838, -0.08584, -0.93342)11.85725, 107.09819, 204.97092
3given(-0.82912, -0.36224, 0.42585), (-0.36433, -0.22767, -0.90301), (0.42406, -0.90385, 0.05679)73.92876, 182.32613, 126.08163

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE


Mass: 68860.742 Da / Num. of mol.: 4
Fragment: DOMAIN 1/: 1-208, DOMAIN 2/: 209-406, DOMAIN 3/: 407-619
Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: O93738, UniProt: Q8U1K3*PLUS

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Non-polymers , 5 types, 200 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-GUA / GLUTARIC ACID / Glutaric acid


Mass: 132.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H8O4
#5: Chemical
ChemComp-PTE / TUNGSTOPTERIN COFACTOR


Mass: 1031.855 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H29MgN10O14P2S4W
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.9 Å3/Da / Density % sol: 56.17 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Method: melting-point capillary method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
155-65 mg/mlprotein11
250 mMTris-HCl11
32.0 mMdithionite11
42 mMdithiothreitol11
50.2 M11KCl
630 %(v/v)glycerol12
720 %(w/v)PEG400012
80.1 Msodium citrate12
90.2 M12NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 93705 / % possible obs: 77.6 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.059 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.158 / % possible all: 40.3
Reflection
*PLUS
Num. measured all: 193320 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 40.3 % / Rmerge(I) obs: 0.158

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AOR

1aor


Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 4589 5 %RANDOM
Rwork0.177 ---
obs0.177 93280 77 %-
Displacement parametersBiso mean: 23.8 Å2
Refine analyzeLuzzati d res low obs: 0 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19144 0 272 184 19600
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.08
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_deg1.29
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.304 282 5 %
Rwork0.27 5858 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
LS refinement shell
*PLUS
Rfactor Rwork: 0.27

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