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- PDB-8wm1: DHS dehydratase -

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Basic information

Entry
Database: PDB / ID: 8wm1
TitleDHS dehydratase
Components3-dehydroshikimate dehydratase (DHS dehydratase)
KeywordsHYDROLASE / dehydratase / right-handed beta-helix / lyase-like
Function / homologyRight handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor / 3-dehydroshikimate dehydratase (DHS dehydratase)
Function and homology information
Biological speciesAcinetobacter pittii PHEA-2 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsWang, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Metab Eng / Year: 2024
Title: Efficient production of protocatechuic acid using systems engineering of Escherichia coli.
Authors: Wang, M. / Wang, H. / Gao, C. / Wei, W. / Liu, J. / Chen, X. / Hu, G. / Song, W. / Wu, J. / Zhang, F. / Liu, L.
History
DepositionOct 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-dehydroshikimate dehydratase (DHS dehydratase)
B: 3-dehydroshikimate dehydratase (DHS dehydratase)
C: 3-dehydroshikimate dehydratase (DHS dehydratase)
D: 3-dehydroshikimate dehydratase (DHS dehydratase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,44412
Polymers207,1234
Non-polymers3218
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.560, 97.670, 132.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
3-dehydroshikimate dehydratase (DHS dehydratase)


Mass: 51780.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter pittii PHEA-2 (bacteria) / Gene: quiC / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: F0KF79
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion
Details: potassium thiocyanate, methoxypoly(ethylene glycol) ~2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: May 6, 2023 / Details: MULTILAYER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.74→47.85 Å / Num. obs: 50016 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.989 / Net I/σ(I): 8
Reflection shellResolution: 2.74→2.82 Å / Rmerge(I) obs: 0.573 / Num. unique obs: 4543

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.74→46.28 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.89 / SU B: 16.042 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25473 2534 5.1 %RANDOM
Rwork0.22357 ---
obs0.22514 47436 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.879 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å20 Å2
2--1.87 Å2-0 Å2
3----2.1 Å2
Refinement stepCycle: 1 / Resolution: 2.74→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13984 0 8 59 14051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213485
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.93819330
X-RAY DIFFRACTIONr_angle_other_deg0.741330955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03751858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.50826.112679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.993152351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4351564
X-RAY DIFFRACTIONr_chiral_restr0.0790.22147
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216929
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8053.0527426
X-RAY DIFFRACTIONr_mcbond_other1.7983.0527425
X-RAY DIFFRACTIONr_mcangle_it3.1124.5719277
X-RAY DIFFRACTIONr_mcangle_other3.1124.5729278
X-RAY DIFFRACTIONr_scbond_it1.4563.1326816
X-RAY DIFFRACTIONr_scbond_other1.4553.1336817
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5584.64710051
X-RAY DIFFRACTIONr_long_range_B_refined4.54834.64315062
X-RAY DIFFRACTIONr_long_range_B_other4.54734.65615056
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A153600.03
12B153600.03
21A153540.03
22C153540.03
31A154060.04
32D154060.04
41B153940.03
42C153940.03
51B153730.03
52D153730.03
61C153840.03
62D153840.03
LS refinement shellResolution: 2.741→2.806 Å
RfactorNum. reflection% reflection
Rfree0.315 188 -
Rwork0.311 3463 -
obs--99.7 %

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