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- PDB-1fwl: CRYSTAL STRUCTURE OF HOMOSERINE KINASE -

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Basic information

Entry
Database: PDB / ID: 1fwl
TitleCRYSTAL STRUCTURE OF HOMOSERINE KINASE
ComponentsHOMOSERINE KINASE
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


homoserine kinase / homoserine kinase activity / threonine biosynthetic process / phosphorylation / 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, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 ...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, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsZhou, T. / Daugherty, M. / Grishin, N.V. / Osterman, A.L. / Zhang, H.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily.
Authors: Zhou, T. / Daugherty, M. / Grishin, N.V. / Osterman, A.L. / Zhang, H.
History
DepositionSep 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: HOMOSERINE KINASE
D: HOMOSERINE KINASE


Theoretical massNumber of molelcules
Total (without water)129,1974
Polymers129,1974
Non-polymers00
Water9,116506
1
A: HOMOSERINE KINASE
B: HOMOSERINE KINASE


Theoretical massNumber of molelcules
Total (without water)64,5992
Polymers64,5992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-27 kcal/mol
Surface area24060 Å2
MethodPISA
2
C: HOMOSERINE KINASE
D: HOMOSERINE KINASE


Theoretical massNumber of molelcules
Total (without water)64,5992
Polymers64,5992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-27 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.993, 128.721, 109.423
Angle α, β, γ (deg.)90.00, 105.57, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer: chain A and B or chain C and D.

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Components

#1: Protein
HOMOSERINE KINASE / HK


Mass: 32299.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: Q58504, homoserine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
250 mMHEPES1drop
3150 mM1dropNaCl
41 mMdithiothreitol1drop
50.1 MTris-HCl1drop
60.2 MNa acetate1drop
725 %PEG40001drop
820 %PEG40001reservoir
90.1 MTris-HCl1reservoir
100.2 MNa acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. all: 78358 / Num. obs: 78267 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 29.2
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 0.309 / Num. unique all: 3827 / % possible all: 96.9
Reflection
*PLUS
Num. measured all: 258313
Reflection shell
*PLUS
% possible obs: 96.9 % / Mean I/σ(I) obs: 3.45

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.25→20 Å / Cross valid method: Free-R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3893 5 %RANDOM
Rwork0.204 ---
all-78358 --
obs-76716 97.9 %-
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9076 0 0 506 9582
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.67

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