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- PDB-7z3s: CRYSTAL STRUCTURE of PheF from Geobacillus stearothermophilus -

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Basic information

Entry
Database: PDB / ID: 7z3s
TitleCRYSTAL STRUCTURE of PheF from Geobacillus stearothermophilus
ComponentsAcetaldehyde dehydrogenase
KeywordsLYASE / LYASE-OXIDOREDUCTASE
Function / homology
Function and homology information


acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / catabolic process / NAD binding
Similarity search - Function
Acetaldehyde dehydrogenase / Acetaldehyde dehydrogenase, C-terminal / Prokaryotic acetaldehyde dehydrogenase, dimerisation / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Acetaldehyde dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsDriller, R. / Haack, M. / Brueck, T. / Loll, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF THE P1 trifluoroethylglycine (TfeGly) BPTI MUTANT- BOVINE CHYMOTRYPSIN COMPLEX
Authors: Leppkes, J. / Wehrhan, L. / Dimos, N. / Loll, B. / Hohmann, T. / Dyrks, M. / Wieseke, A. / Wahl, M.C. / Keller, B.G. / Koksch, B.
History
DepositionMar 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1564
Polymers31,8711
Non-polymers2853
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.250, 69.250, 88.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Acetaldehyde dehydrogenase / Acetaldehyde dehydrogenase [acetylating]


Mass: 31870.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: pheF / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B0VXM6, acetaldehyde dehydrogenase (acetylating)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15 M di-Ammonium hydrogen phosphate 15% PEG3350 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.99→35 Å / Num. obs: 28151 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 43.54 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.086 / Net I/σ(I): 18.3
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 13.1 % / Num. unique obs: 4169 / CC1/2: 0.57 / Rrim(I) all: 1.539

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NVM

1nvm


Resolution: 1.99→34.62 Å / SU ML: 0.2486 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 23.5486
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2105 1976 7.02 %
Rwork0.1808 26164 -
obs0.1829 28140 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.51 Å2
Refinement stepCycle: LAST / Resolution: 1.99→34.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 15 53 2264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122292
X-RAY DIFFRACTIONf_angle_d1.23583116
X-RAY DIFFRACTIONf_chiral_restr0.0703372
X-RAY DIFFRACTIONf_plane_restr0.0087398
X-RAY DIFFRACTIONf_dihedral_angle_d7.3619323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.34311180.31451546X-RAY DIFFRACTION81.41
2.04-2.10.28771420.26551894X-RAY DIFFRACTION100
2.1-2.160.31091460.24531873X-RAY DIFFRACTION99.95
2.16-2.230.29481380.22721900X-RAY DIFFRACTION99.95
2.23-2.310.25181450.20091875X-RAY DIFFRACTION99.8
2.31-2.40.29751430.20261885X-RAY DIFFRACTION99.95
2.4-2.510.24771450.19631874X-RAY DIFFRACTION100
2.51-2.640.24861390.21511896X-RAY DIFFRACTION99.85
2.64-2.810.26361380.22221896X-RAY DIFFRACTION99.85
2.81-3.020.23461440.2111889X-RAY DIFFRACTION99.95
3.02-3.330.23951460.21011892X-RAY DIFFRACTION100
3.33-3.810.21031480.1851896X-RAY DIFFRACTION99.95
3.81-4.80.14341390.1371906X-RAY DIFFRACTION100
4.8-34.620.17091450.14071942X-RAY DIFFRACTION99.81
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.78736120349-0.402396816527-0.3642746230511.8121965747-1.050955951661.40606233975-0.159923776481-0.0665428885777-0.160165018838-0.0531401492764-0.0346780877232-0.1648731770740.1533392248430.0602775710754-1.04972022268E-50.3971209671840.02627248565550.07255147681420.3514755983670.02575233995080.40873345988234.1065643409-1.1562938643845.5008943324
23.22068958794-1.81354129771-0.612300129722.287528375060.26097564541.40539100656-0.1486711054840.0926804690208-0.09849554666370.1225043447810.02716953822140.1331786276040.00389006263124-0.1973309591790.0001168583707230.3661262809350.01574970501640.009336679287350.366934991449-0.01110388163190.32146915985817.988046323716.889055423344.0823380891
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain A and resid -3:122-3 - 1221 - 126
22chain A and resid 123:292123 - 292127 - 290

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