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- PDB-4qgs: Substrate and cofactor-free form of the Aldehyde Reductase YqhD f... -

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Basic information

Entry
Database: PDB / ID: 4qgs
TitleSubstrate and cofactor-free form of the Aldehyde Reductase YqhD from E. coli.
ComponentsAlcohol dehydrogenase YqhD
KeywordsOXIDOREDUCTASE / NADPH-dependent Aldehyde reductase
Function / homology
Function and homology information


alcohol dehydrogenase [NAD(P)+] activity / methylglyoxal reductase (NADPH) (acetol producing) activity / butanol dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) / alcohol dehydrogenase (NADP+) activity / response to reactive oxygen species / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Butanol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle ...Butanol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Alcohol dehydrogenase YqhD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLaMattina, J.W. / Kapoor, S. / Lanzilotta, W.N.
CitationJournal: To be Published
Title: Open form of E. coli YqhD
Authors: LaMattina, J.W. / Kapoor, S. / Gouvea, I. / Slovic, A. / Lanzilotta, W.N.
History
DepositionMay 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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_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_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_ref_seq_dif.details / _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: Alcohol dehydrogenase YqhD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5413
Polymers43,4401
Non-polymers1012
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Alcohol dehydrogenase YqhD
hetero molecules

A: Alcohol dehydrogenase YqhD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0826
Polymers86,8802
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_754-x+2,y,-z-11
Buried area3720 Å2
ΔGint-98 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.402, 68.441, 66.602
Angle α, β, γ (deg.)90.00, 118.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alcohol dehydrogenase YqhD


Mass: 43440.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yqhD, b3011, JW2978
References: UniProt: Q46856, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.3 M NaCl, 25 % (w/v) PEG 3000, and 0.1 M TRIS, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 18, 2012
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 35

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1639) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→32.668 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 22.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 3882 4.61 %Random
Rwork0.186 ---
all0.19 87508 --
obs0.1875 84210 96.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→32.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 0 2 267 3190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083017
X-RAY DIFFRACTIONf_angle_d1.1494103
X-RAY DIFFRACTIONf_dihedral_angle_d13.5861099
X-RAY DIFFRACTIONf_chiral_restr0.047470
X-RAY DIFFRACTIONf_plane_restr0.005536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72070.28711100.24842323X-RAY DIFFRACTION79
1.7207-1.74250.3183880.22982513X-RAY DIFFRACTION82
1.7425-1.76540.24341290.23142653X-RAY DIFFRACTION88
1.7654-1.78960.26871360.21522669X-RAY DIFFRACTION91
1.7896-1.81520.28721340.20392787X-RAY DIFFRACTION93
1.8152-1.84230.2291250.20722847X-RAY DIFFRACTION96
1.8423-1.87110.22291380.20142886X-RAY DIFFRACTION97
1.8711-1.90170.24161540.19332893X-RAY DIFFRACTION97
1.9017-1.93450.19021430.19312879X-RAY DIFFRACTION98
1.9345-1.96970.24051450.20142935X-RAY DIFFRACTION98
1.9697-2.00760.23191400.2022934X-RAY DIFFRACTION98
2.0076-2.04860.24661360.18632934X-RAY DIFFRACTION99
2.0486-2.09310.22571350.18052929X-RAY DIFFRACTION98
2.0931-2.14180.20071590.1922956X-RAY DIFFRACTION98
2.1418-2.19530.23611410.18062908X-RAY DIFFRACTION99
2.1953-2.25470.23861420.17642907X-RAY DIFFRACTION99
2.2547-2.3210.18641480.1832942X-RAY DIFFRACTION99
2.321-2.39590.18581210.18232979X-RAY DIFFRACTION99
2.3959-2.48150.23681680.18462939X-RAY DIFFRACTION99
2.4815-2.58080.24211400.19372936X-RAY DIFFRACTION99
2.5808-2.69820.23581530.19972950X-RAY DIFFRACTION99
2.6982-2.84040.23441450.19982954X-RAY DIFFRACTION99
2.8404-3.01820.22331540.19722930X-RAY DIFFRACTION99
3.0182-3.25110.21491380.193018X-RAY DIFFRACTION100
3.2511-3.57790.22351480.18222959X-RAY DIFFRACTION100
3.5779-4.09480.19191450.16272976X-RAY DIFFRACTION100
4.0948-5.15570.17031410.15652963X-RAY DIFFRACTION100
5.1557-32.67390.24761260.19342829X-RAY DIFFRACTION94

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