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- PDB-5was: Corynebacterium glutamicum Hydrolyzed Homoserine kinase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5was
TitleCorynebacterium glutamicum Hydrolyzed Homoserine kinase
Components(Homoserine kinase) x 3
KeywordsTRANSFERASE / Corynebacterium glutamicum / Homoserine Kinase / L-threonine / L-homoserine / Magnesium
Function / homology
Function and homology information


homoserine kinase / homoserine kinase activity / threonine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Homoserine kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
PHOSPHATE ION / Homoserine kinase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsPetit, C. / Ronning, D.R.
CitationJournal: ACS Omega / Year: 2018
Title: Reduction of Feedback Inhibition in Homoserine Kinase (ThrB) ofCorynebacterium glutamicumEnhances l-Threonine Biosynthesis.
Authors: Petit, C. / Kim, Y. / Lee, S.K. / Brown, J. / Larsen, E. / Ronning, D.R. / Suh, J.W. / Kang, C.M.
History
DepositionJun 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homoserine kinase
B: Homoserine kinase
C: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6104
Polymers33,5153
Non-polymers951
Water1,09961
1
A: Homoserine kinase
B: Homoserine kinase
C: Homoserine kinase
hetero molecules

A: Homoserine kinase
B: Homoserine kinase
C: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2208
Polymers67,0306
Non-polymers1902
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13300 Å2
ΔGint-88 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.227, 46.227, 267.295
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Homoserine kinase / HSK


Mass: 18769.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: thrB, Cgl1184, cg1338 / Production host: Escherichia coli BL21 / References: UniProt: P07128, homoserine kinase
#2: Protein Homoserine kinase / HSK


Mass: 6464.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: thrB, Cgl1184, cg1338 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P07128, homoserine kinase
#3: Protein Homoserine kinase / HSK


Mass: 8281.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: thrB, Cgl1184, cg1338 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P07128, homoserine kinase
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The CglThrB protein concentrated to 16.2 mg/mL in 20 mM Tris pH 7.5, 150 mM NaCl, 50 mM KCl and 50 mM MgCl2 was used for crystallization experiments. Drops were equilibrated against a 100 ...Details: The CglThrB protein concentrated to 16.2 mg/mL in 20 mM Tris pH 7.5, 150 mM NaCl, 50 mM KCl and 50 mM MgCl2 was used for crystallization experiments. Drops were equilibrated against a 100 microLitter of well solution containing 0.25 M ammonium sulfate, 25 % PEG 3,350 and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.799→50 Å / Num. obs: 27709 / % possible obs: 97.8 % / Redundancy: 23.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 43.7
Reflection shellHighest resolution: 1.8 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 2537 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WAT

5wat


Resolution: 1.799→34.967 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 34.36
RfactorNum. reflection% reflection
Rfree0.2871 1994 7.22 %
Rwork0.2414 --
obs0.2448 27614 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.799→34.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 5 61 2113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062098
X-RAY DIFFRACTIONf_angle_d1.0432869
X-RAY DIFFRACTIONf_dihedral_angle_d14.117752
X-RAY DIFFRACTIONf_chiral_restr0.039341
X-RAY DIFFRACTIONf_plane_restr0.005381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.799-1.8440.41341300.31391673X-RAY DIFFRACTION90
1.844-1.89380.34281350.30031735X-RAY DIFFRACTION97
1.8938-1.94950.3691380.33261761X-RAY DIFFRACTION96
1.9495-2.01240.31761370.29241786X-RAY DIFFRACTION97
2.0124-2.08440.34831390.27021780X-RAY DIFFRACTION98
2.0844-2.16780.29641400.27591799X-RAY DIFFRACTION98
2.1678-2.26650.33331400.27841786X-RAY DIFFRACTION98
2.2665-2.38590.3921420.28331823X-RAY DIFFRACTION98
2.3859-2.53540.32261430.28681844X-RAY DIFFRACTION99
2.5354-2.7310.3341470.27421887X-RAY DIFFRACTION100
2.731-3.00570.3151450.27251856X-RAY DIFFRACTION100
3.0057-3.44040.29421480.24751914X-RAY DIFFRACTION100
3.4404-4.33320.25531510.21251941X-RAY DIFFRACTION100
4.3332-34.97350.23661590.19842035X-RAY DIFFRACTION96

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