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- PDB-5zxl: Structure of GldA from E.coli -

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Basic information

Entry
Database: PDB / ID: 5zxl
TitleStructure of GldA from E.coli
ComponentsGlycerol dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / Glycerol / Catalytic
Function / homology
Function and homology information


(R)-aminopropanol dehydrogenase / (R)-aminopropanol dehydrogenase activity / anaerobic glycerol catabolic process / methylglyoxal catabolic process / glycerol dehydrogenase / glycerol dehydrogenase (NAD+) activity / protein homotetramerization / protein-containing complex / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle ...Glycerol dehydrogenase / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type, conserved site / 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
Glycerol dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.794 Å
AuthorsZhang, J. / Lin, L.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: Structure of glycerol dehydrogenase (GldA) from Escherichia coli.
Authors: Zhang, J. / Nanjaraj Urs, A.N. / Lin, L. / Zhou, Y. / Hu, Y. / Hua, G. / Gao, Q. / Yuchi, Z. / Zhang, Y.
History
DepositionMay 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerol dehydrogenase
B: Glycerol dehydrogenase
C: Glycerol dehydrogenase
D: Glycerol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,93227
Polymers154,9844
Non-polymers1,94823
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-249 kcal/mol
Surface area51750 Å2
Unit cell
Length a, b, c (Å)162.446, 162.446, 293.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 29 or (resid 30...
21(chain B and (resid 1 through 29 or (resid 30...
31(chain C and (resid 1 through 45 or (resid 46...
41(chain D and (resid 1 through 30 or (resid 31...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALA(chain A and (resid 1 through 29 or (resid 30...AA1 - 291 - 29
12GLUGLUARGARG(chain A and (resid 1 through 29 or (resid 30...AA30 - 3130 - 31
13METMETGLUGLU(chain A and (resid 1 through 29 or (resid 30...AA1 - 3671 - 367
14METMETGLUGLU(chain A and (resid 1 through 29 or (resid 30...AA1 - 3671 - 367
15METMETGLUGLU(chain A and (resid 1 through 29 or (resid 30...AA1 - 3671 - 367
16METMETGLUGLU(chain A and (resid 1 through 29 or (resid 30...AA1 - 3671 - 367
21METMETALAALA(chain B and (resid 1 through 29 or (resid 30...BB1 - 291 - 29
22GLUGLUARGARG(chain B and (resid 1 through 29 or (resid 30...BB30 - 3130 - 31
23METMETGLUGLU(chain B and (resid 1 through 29 or (resid 30...BB1 - 3671 - 367
24METMETGLUGLU(chain B and (resid 1 through 29 or (resid 30...BB1 - 3671 - 367
25METMETGLUGLU(chain B and (resid 1 through 29 or (resid 30...BB1 - 3671 - 367
26METMETGLUGLU(chain B and (resid 1 through 29 or (resid 30...BB1 - 3671 - 367
31METMETGLNGLN(chain C and (resid 1 through 45 or (resid 46...CC1 - 451 - 45
32SERSERSERSER(chain C and (resid 1 through 45 or (resid 46...CC4646
33METMETGLUGLU(chain C and (resid 1 through 45 or (resid 46...CC1 - 3671 - 367
34METMETGLUGLU(chain C and (resid 1 through 45 or (resid 46...CC1 - 3671 - 367
35METMETGLUGLU(chain C and (resid 1 through 45 or (resid 46...CC1 - 3671 - 367
41METMETGLUGLU(chain D and (resid 1 through 30 or (resid 31...DD1 - 301 - 30
42ARGARGARGARG(chain D and (resid 1 through 30 or (resid 31...DD3131
43METMETGLUGLU(chain D and (resid 1 through 30 or (resid 31...DD1 - 3671 - 367
44METMETGLUGLU(chain D and (resid 1 through 30 or (resid 31...DD1 - 3671 - 367
45METMETGLUGLU(chain D and (resid 1 through 30 or (resid 31...DD1 - 3671 - 367

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glycerol dehydrogenase / GLDH


Mass: 38746.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: gldA, b3945, JW5556 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9S5, glycerol dehydrogenase

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Non-polymers , 5 types, 161 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 138 / 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: 5.85 Å3/Da / Density % sol: 79 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.02M Tris-HCl(pH7.4), 0.05mM sodium chloride, 0.15mM ammonium acetate

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.79→40.611 Å / Num. obs: 97055 / % possible obs: 60 % / Redundancy: 1 % / Biso Wilson estimate: 63.98 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.83
Reflection shellResolution: 2.794→2.894 Å / Rmerge(I) obs: 0.722 / Num. unique obs: 9400

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MCA

4mca


Resolution: 2.794→40.611 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21
RfactorNum. reflection% reflection
Rfree0.2043 2000 2.06 %
Rwork0.1734 --
obs0.1741 97055 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.61 Å2 / Biso mean: 62.0152 Å2 / Biso min: 26.53 Å2
Refinement stepCycle: final / Resolution: 2.794→40.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10743 0 199 138 11080
Biso mean--112.17 55.58 -
Num. residues----1468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811036
X-RAY DIFFRACTIONf_angle_d0.97815017
X-RAY DIFFRACTIONf_chiral_restr0.0561762
X-RAY DIFFRACTIONf_plane_restr0.0071963
X-RAY DIFFRACTIONf_dihedral_angle_d16.6376555
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6453X-RAY DIFFRACTION13.823TORSIONAL
12B6453X-RAY DIFFRACTION13.823TORSIONAL
13C6453X-RAY DIFFRACTION13.823TORSIONAL
14D6453X-RAY DIFFRACTION13.823TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7936-2.86350.29411380.25616530666897
2.8635-2.94090.29151410.246467016842100
2.9409-3.02740.32091410.24667476888100
3.0274-3.12510.30251420.236567356877100
3.1251-3.23670.26041420.224267426884100
3.2367-3.36630.25641420.219967436885100
3.3663-3.51940.2181410.188967636904100
3.5194-3.70480.20551440.174268106954100
3.7048-3.93680.19621420.161967606902100
3.9368-4.24040.18181440.14268236967100
4.2404-4.66660.15091430.129368316974100
4.6666-5.34060.17181450.146468697014100
5.3406-6.72360.19331460.17926924707099
6.7236-40.61580.18431490.15667077722697

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