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- PDB-1m6w: Binary complex of Human glutathione-dependent formaldehyde dehydr... -

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Basic information

Entry
Database: PDB / ID: 1m6w
TitleBinary complex of Human glutathione-dependent formaldehyde dehydrogenase and 12-Hydroxydodecanoic acid
ComponentsGlutathione-dependent formaldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Glutathione-dependent formaldehyde dehydrogenase / Class III alcohol dehydrogenase
Function / homology
Function and homology information


formaldehyde dehydrogenase activity / S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD(P)+) activity / fatty acid omega-oxidation / formaldehyde catabolic process / respiratory system process / response to nitrosative stress / Ethanol oxidation ...formaldehyde dehydrogenase activity / S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD(P)+) activity / fatty acid omega-oxidation / formaldehyde catabolic process / respiratory system process / response to nitrosative stress / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / positive regulation of blood pressure / alcohol dehydrogenase / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / response to redox state / retinoid metabolic process / 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
12-HYDROXYDODECANOIC ACID / : / PHOSPHATE ION / Alcohol dehydrogenase class-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 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 17, 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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)80,33913
Polymers79,2822
Non-polymers1,05711
Water12,016667
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-103 kcal/mol
Surface area27740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.632, 78.632, 309.417
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

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 678 molecules

#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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-12H / 12-HYDROXYDODECANOIC ACID


Mass: 216.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 59.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: PEG 8000, Potassium phosphate, zinc sulphate, Dithiothreitol, pH 7.1, 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.2667, 1.2827, 1.2837
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 24, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.26671
21.28271
31.28371
ReflectionResolution: 2.3→20 Å / Num. all: 44550 / Num. obs: 43971 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 23.6 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 37.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 7.5 / Num. unique all: 3959 / % possible all: 90.6
Reflection
*PLUS
Rmerge(I) obs: 0.092
Reflection shell
*PLUS
Rmerge(I) obs: 0.288

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2278 5.2 %RANDOM
Rwork0.191 ---
all0.1929 44335 --
obs0.191 43801 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.5362 Å2 / ksol: 0.353865 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 51 667 6262
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 235 5.7 %
Rwork0.2031 6391 -
obs-3725 90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Rfactor all: 0.1929 / Rfactor obs: 0.191 / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Rfactor Rfree: 0.25 / Rfactor Rwork: 0.2031

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