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- PDB-1m6h: Human glutathione-dependent formaldehyde dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 1m6h
TitleHuman glutathione-dependent formaldehyde dehydrogenase
ComponentsGlutathione-dependent formaldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / glutathione-dependent formaldehyde dehydrogenase class III alcohol dehydrogenase
Function / homology
Function and homology information


formaldehyde dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase / fatty acid omega-oxidation / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / response to nitrosative stress / formaldehyde catabolic process / Ethanol oxidation / : ...formaldehyde dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase / fatty acid omega-oxidation / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / response to nitrosative stress / formaldehyde catabolic process / Ethanol oxidation / : / respiratory system process / positive regulation of blood pressure / alcohol dehydrogenase / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / retinoid metabolic process / response to redox state / fatty acid binding / response to lipopolysaccharide / electron transfer activity / mitochondrion / extracellular exosome / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Alcohol dehydrogenase class III / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily ...Alcohol dehydrogenase class III / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Alcohol dehydrogenase class-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSanghani, P.C. / Robinson, H. / Bosron, W.F. / Hurley, T.D.
CitationJournal: Biochemistry / Year: 2002
Title: Human glutathione-dependent formaldehyde dehydrogenase. Structures of apo, binary, and inhibitory ternary complexes.
Authors: Sanghani, P.C. / Robinson, H. / Bosron, W.F. / Hurley, T.D.
History
DepositionJul 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Glutathione-dependent formaldehyde dehydrogenase
B: Glutathione-dependent formaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,09713
Polymers79,2822
Non-polymers81511
Water16,123895
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-117 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.620, 78.620, 309.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein Glutathione-dependent formaldehyde dehydrogenase / E.C.1.1.1.1 / alcohol dehydrogenase class III chi chain / Alcohol dehydrogenase (class III) / chi polypeptide / ...alcohol dehydrogenase class III chi chain / Alcohol dehydrogenase (class III) / chi polypeptide / FDH / E.C.1.2.1.1


Mass: 39641.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Apoenzyme / Source: (gene. exp.) Homo sapiens (human) / Gene: ADH5 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1 / References: UniProt: P11766, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 895 / 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: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: PEG 8000, Potassium phosphate, Zinc chloride, Dithiotreitol, pH 6.9, VAPOR DIFFUSION, SITTING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / PH range low: 7.1 / PH range high: 6.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115-20 mg/mlenzyme1drop
20.1 Mpotassium phosphate1reservoirpH6.9-7.1
30.100 mM1reservoirZnSO4
41 mMdithiothreitol1reservoir
512-15 %PEG80001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9790,1.2770,1.2833,1.2882
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 21, 2001
ADSC QUANTUM 42CCDMar 9, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.2771
31.28331
41.28821
ReflectionResolution: 2→30 Å / Num. all: 67142 / Num. obs: 64501 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 24
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 4.3 / Num. unique all: 5783 / Rsym value: 0.462 / % possible all: 87.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 508528 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 87.6 % / Rmerge(I) obs: 0.438

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3241 -RANDOM
Rwork0.185 ---
all0.187 64379 --
obs0.187 64379 96.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 31 895 6470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
LS refinement shellResolution: 2→30 Å
RfactorNum. reflection% reflection
Rfree0.218 3241 -
Rwork0.185 --
obs-64379 96.1 %
Refinement
*PLUS
Rfactor obs: 0.187 / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.218 / Rfactor Rwork: 0.185

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