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- PDB-2fzw: Structure of the binary complex of the E67L mutant of human gluta... -

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Basic information

Entry
Database: PDB / ID: 2fzw
TitleStructure of the binary complex of the E67L mutant of human glutathione-dependent formaldehyde dehydrogenase with NAD(H)
ComponentsAlcohol dehydrogenase class III chi chain
KeywordsOXIDOREDUCTASE / s-nitrosoglutathione reductase / glutathione-dependent formaldehyde 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
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Alcohol dehydrogenase class-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsSanghani, P.C. / Robinson, H.
CitationJournal: Biochemistry / Year: 2006
Title: Structure-function relationships in human glutathione-dependent formaldehyde dehydrogenase. Role of Glu-67 and Arg-368 in the catalytic mechanism.
Authors: Sanghani, P.C. / Davis, W.I. / Zhai, L. / Robinson, H.
History
DepositionFeb 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase class III chi chain
B: Alcohol dehydrogenase class III chi chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,20213
Polymers79,2502
Non-polymers1,95211
Water18,3931021
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-116 kcal/mol
Surface area28080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.270, 79.270, 311.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase class III chi chain / S- hydroxymethyl / glutathione dehydrogenase / Glutathione- dependent formaldehyde dehydrogenase / FDH


Mass: 39625.043 Da / Num. of mol.: 2 / Fragment: Glutathione-dependent formaldehyde dehydrogenase / Mutation: E67L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADH5, ADHX, FDH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P11766, alcohol dehydrogenase, S-(hydroxymethyl)glutathione dehydrogenase

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Non-polymers , 5 types, 1032 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1021 / 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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 15% PEG 8000, 100mM potassium phosphate, pH 7.1, 10uM Zinc sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. all: 87310 / Num. obs: 87310 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.3 % / Rmerge(I) obs: 0.1 / Χ2: 1.471 / Net I/σ(I): 8.7
Reflection shellResolution: 1.84→1.91 Å / % possible obs: 99.4 % / Redundancy: 26.2 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 9 / Num. unique all: 8508 / Num. unique obs: 8508 / Χ2: 0.891 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→50 Å / FOM work R set: 0.885 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 4402 5 %Random
Rwork0.177 ---
all-87310 --
obs-87208 99.7 %-
Solvent computationBsol: 46.474 Å2
Displacement parametersBiso mean: 20.171 Å2
Baniso -1Baniso -2Baniso -3
1--3.216 Å20 Å20 Å2
2---3.216 Å20 Å2
3---6.432 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.84→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5661 0 109 1021 6791
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONrmsd bonds0.0049
X-RAY DIFFRACTIONrmsd angles1.5
X-RAY DIFFRACTIONrmsd dihedrals24
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.84-1.850.262770.22914771554
1.85-1.870.186840.19316221706
1.87-1.880.243850.2116241709
1.88-1.890.2121000.20216331733
1.89-1.910.217730.18716321705
1.91-1.920.258800.19316021682
1.92-1.930.215820.18716741756
1.93-1.950.202940.1715931687
1.95-1.970.189930.17816101703
1.97-1.980.21910.17516551746
1.98-20.247850.1816061691
2-2.020.1941140.16616001714
2.02-2.030.184910.16716661757
2.03-2.050.215730.17216031676
2.05-2.070.216910.16716451736
2.07-2.090.198870.17516321719
2.09-2.110.183820.16716211703
2.11-2.140.192970.16816481745
2.14-2.160.243690.1816571726
2.16-2.180.217980.16816111709
2.18-2.210.226860.18116481734
2.21-2.230.243760.1816241700
2.23-2.260.223840.17116811765
2.26-2.290.2231030.17316111714
2.29-2.320.227880.17516401728
2.32-2.350.216900.16216511741
2.35-2.380.188710.16216691740
2.38-2.420.196970.16516361733
2.42-2.460.223850.17716511736
2.46-2.50.224860.18216691755
2.5-2.540.2790.17516421721
2.54-2.590.216870.1916471734
2.59-2.640.224990.18816661765
2.64-2.690.22910.18216351726
2.69-2.750.245960.1916691765
2.75-2.810.1961040.18716511755
2.81-2.880.221690.19516731742
2.88-2.960.21050.19816671772
2.96-3.050.226860.19416701756
3.05-3.150.186810.18616741755
3.15-3.260.213890.18816691758
3.26-3.390.215890.18116921781
3.39-3.540.183830.16516881771
3.54-3.730.173900.16616991789
3.73-3.960.185880.16217121800
3.96-4.270.167960.14716871783
4.27-4.70.12850.13417391824
4.7-5.380.208830.16817481831
5.38-6.770.2251120.19717561868
6.77-500.237780.22119312009
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4nadh.parnadh.top

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