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- PDB-1fdo: OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1fdo
TitleOXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI
ComponentsFORMATE DEHYDROGENASE H
KeywordsOXIDOREDUCTASE / SELENIUM / SELENOCYSTEINE / SECYS / MOLYBDENUM / MOLYBDOPTERIN / MPT / MOLYBDOPTERIN GUANINE DINUCLEOTIDE / MGD / IRON SULFUR CLUSTER / FE4S4 / FORMATE / DEHYDROGENASE / ANAEROBIC
Function / homology
Function and homology information


formate dehydrogenase (hydrogenase) / formate oxidation / oxidoreductase activity, acting on the aldehyde or oxo group of donors / formate dehydrogenase complex / glucose catabolic process / formate dehydrogenase (NAD+) activity / anaerobic electron transport chain / urate catabolic process / molybdopterin cofactor binding / anaerobic respiration ...formate dehydrogenase (hydrogenase) / formate oxidation / oxidoreductase activity, acting on the aldehyde or oxo group of donors / formate dehydrogenase complex / glucose catabolic process / formate dehydrogenase (NAD+) activity / anaerobic electron transport chain / urate catabolic process / molybdopterin cofactor binding / anaerobic respiration / respiratory electron transport chain / 4 iron, 4 sulfur cluster binding / metal ion binding / membrane / cytosol
Similarity search - Function
Formate dehydrogenase H, molybdopterin-binding domain / Single helix bin / ADC-like domains / Rossmann fold - #740 / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, molybdopterin cofactor binding site ...Formate dehydrogenase H, molybdopterin-binding domain / Single helix bin / ADC-like domains / Rossmann fold - #740 / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / N-terminal domain of TfIIb / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Single Sheet / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Chem-MGD / IRON/SULFUR CLUSTER / Formate dehydrogenase H
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER ANALYSIS USING PHASES FROM THE STRUCTURE OF REDUCED FDH-H (PDB ENTRY 1AA6) / Resolution: 2.8 Å
AuthorsSun, P.D. / Boyington, J.C.
Citation
Journal: Science / Year: 1997
Title: Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster.
Authors: Boyington, J.C. / Gladyshev, V.N. / Khangulov, S.V. / Stadtman, T.C. / Sun, P.D.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Characterization of Crystalline Formate Dehydrogenase H from Escherichia Coli. Stabilization, Epr Spectroscopy, and Preliminary Crystallographic Analysis
Authors: Gladyshev, V.N. / Boyington, J.C. / Khangulov, S.V. / Grahame, D.A. / Stadtman, T.C. / Sun, P.D.
History
DepositionJan 27, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 29, 2014Group: Structure summary
Revision 1.4Aug 6, 2014Group: Derived calculations / Structure summary
Revision 1.5Feb 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_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.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_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_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_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: FORMATE DEHYDROGENASE H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3945
Polymers79,4661
Non-polymers1,9294
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.600, 146.600, 81.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein FORMATE DEHYDROGENASE H / FDH-H


Mass: 79465.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: OXIDIZED FORM (MO(VI),FE4S4(OX)) OF FDH-H / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: FM911 / Description: FDH-H WAS EXPRESSED ANAEROBICALLY / Gene: FDHF / Plasmid: PFM20 / Production host: Escherichia coli (E. coli) / References: UniProt: P07658, formate dehydrogenase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#4: Chemical ChemComp-6MO / MOLYBDENUM(VI) ION


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion - hanging drop in anaerobic atmosphere
pH: 7.5
Details: FDH-H WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION IN AN ANAEROBIC ATMOSPHERE IN THE PRESENCE OF 1.5 M AMMONIUM SULFATE, 1% PEG 400, 20 MM SODIUM FORMATE AND 100 MM HEPES/NAOH AT PH 7.5. ...Details: FDH-H WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION IN AN ANAEROBIC ATMOSPHERE IN THE PRESENCE OF 1.5 M AMMONIUM SULFATE, 1% PEG 400, 20 MM SODIUM FORMATE AND 100 MM HEPES/NAOH AT PH 7.5. PRIOR TO FREEZING IN LIQUID NITROGEN, CRYSTALS WERE OXIDIZED BY SOAKING IN 10 MM BENZYL VIOLOGEN FOR 30 MINUTES., vapor diffusion - hanging drop in anaerobic atmosphere
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 mg/mlprotein1drop
21.5-1.7 Mammonium sulfate1reservoir
31 %PEG4001reservoir
420 mMsodium formate1reservoir
5100 mMHEPES/NaOH1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 20861 / % possible obs: 93.4 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.1
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.4 / % possible all: 91.4
Reflection
*PLUS
Num. measured all: 84166

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER ANALYSIS USING PHASES FROM THE STRUCTURE OF REDUCED FDH-H (PDB ENTRY 1AA6)
Resolution: 2.8→6 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.281 849 4.7 %RANDOM
Rwork0.192 ---
obs0.192 18013 90 %-
Displacement parametersBiso mean: 23.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5575 0 103 64 5742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.54
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2.5
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.8→2.89 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.33 69 4.3 %
Rwork0.231 1518 -
obs--77.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / 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_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.54
LS refinement shell
*PLUS
Rfactor obs: 0.231

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