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- PDB-5wat: Corynebacterium glutamicum Full length Homoserine kinase -

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Basic information

Entry
Database: PDB / ID: 5wat
TitleCorynebacterium glutamicum Full length Homoserine kinase
ComponentsHomoserine kinase
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: 2.141 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,40514
Polymers66,9582
Non-polymers1,44712
Water3,585199
1
B: Homoserine kinase
hetero molecules

A: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,40514
Polymers66,9582
Non-polymers1,44712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544x+1/2,-y-1/2,-z-1/21
Buried area4620 Å2
ΔGint-98 kcal/mol
Surface area26560 Å2
MethodPISA
2
A: Homoserine kinase
hetero molecules

A: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,09018
Polymers66,9582
Non-polymers2,13216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6200 Å2
ΔGint-142 kcal/mol
Surface area25830 Å2
MethodPISA
3
B: Homoserine kinase
hetero molecules

B: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,71910
Polymers66,9582
Non-polymers7628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-11
Buried area4680 Å2
ΔGint-66 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.081, 130.078, 195.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Homoserine kinase / HSK


Mass: 33478.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: thrB, Cgl1184, cg1338 / Production host: Escherichia coli (E. coli) / References: UniProt: P07128, homoserine kinase

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Non-polymers , 5 types, 211 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 3.32 Å3/Da / Density % sol: 62.99 % / Description: Diamond shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein in 20 mM Tris pH 7.5, 150 mM NaCl, 50 mM KCl and 50 mM MgCl2 well solution: 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 300 mm CCD / Detector: CCD / Date: Feb 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.141→50 Å / Num. obs: 48115 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 20.6
Reflection shellResolution: 2.141→42.34 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 4566 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rpf

4rpf


Resolution: 2.141→42.335 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 2409 5.01 %
Rwork0.1891 --
obs0.1909 48097 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.141→42.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4522 0 78 199 4799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094748
X-RAY DIFFRACTIONf_angle_d1.1346504
X-RAY DIFFRACTIONf_dihedral_angle_d15.031709
X-RAY DIFFRACTIONf_chiral_restr0.047770
X-RAY DIFFRACTIONf_plane_restr0.006855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1413-2.1850.25731330.20982469X-RAY DIFFRACTION92
2.185-2.23250.24421400.20092671X-RAY DIFFRACTION100
2.2325-2.28450.21921400.18922646X-RAY DIFFRACTION100
2.2845-2.34160.25731400.18492662X-RAY DIFFRACTION100
2.3416-2.40490.23961410.18762683X-RAY DIFFRACTION100
2.4049-2.47560.20761400.18642657X-RAY DIFFRACTION100
2.4756-2.55550.21621420.17872687X-RAY DIFFRACTION100
2.5555-2.64690.22341410.18372685X-RAY DIFFRACTION100
2.6469-2.75280.23881400.19292660X-RAY DIFFRACTION100
2.7528-2.87810.251420.1982694X-RAY DIFFRACTION100
2.8781-3.02980.22781420.21112684X-RAY DIFFRACTION100
3.0298-3.21950.2521420.20432721X-RAY DIFFRACTION100
3.2195-3.4680.24271420.19652684X-RAY DIFFRACTION100
3.468-3.81680.26831430.19622728X-RAY DIFFRACTION100
3.8168-4.36860.21151450.172732X-RAY DIFFRACTION100
4.3686-5.50210.20141440.17132750X-RAY DIFFRACTION100
5.5021-42.34350.18811520.1942875X-RAY DIFFRACTION100

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