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- PDB-1h72: CRYSTAL STRUCTURE OF HOMOSERINE KINASE COMPLEXED WITH HSE -

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Basic information

Entry
Database: PDB / ID: 1h72
TitleCRYSTAL STRUCTURE OF HOMOSERINE KINASE COMPLEXED WITH HSE
ComponentsHOMOSERINE KINASE
KeywordsTRANSFERASE / KINASE / THREONINE BIOSYNTHESIS
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, 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / L-HOMOSERINE / Homoserine kinase
Similarity search - Component
Biological speciesMETHANOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKrishna, S.S. / Zhou, T. / Daugherty, M. / Osterman, A.L. / Zhang, H.
Citation
Journal: Biochemistry / Year: 2001
Title: Structural Basis for the Catalysis and Substrate Specificity of Homoserine Kinase
Authors: Krishna, S.S. / Zhou, T. / Daugherty, M. / Osterman, A.L. / Zhang, H.
#1: Journal: Structure / 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
DepositionJul 2, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: HOMOSERINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0474
Polymers32,2991
Non-polymers7473
Water5,549308
1
C: HOMOSERINE KINASE
hetero molecules

C: HOMOSERINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0948
Polymers64,5992
Non-polymers1,4956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)87.990, 87.990, 99.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsTHE CHAIN IN THE COMPLEX IS 1422.9TROM **2

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Components

#1: Protein HOMOSERINE KINASE / HK


Mass: 32299.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCOCCUS JANNASCHII (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q58504, homoserine kinase
#2: Chemical ChemComp-HSE / L-HOMOSERINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growpH: 8 / Details: PEG4000, SODIUM ACETATE, pH 8.00
Crystal grow
*PLUS
Temperature: 100 K / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotease1drop
250 mMHEPES1drop
3150 mM1dropNaCl
45 mM1dropMgCl2
51 mMdithiothreitol1drop
65 mMsubstrate1drop
70.1 MTris1reservoir
80.2 Msodium acetate1reservoir
920-25 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 36728 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 21.1
Reflection
*PLUS
Num. measured all: 206493
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FWL

1fwl


Resolution: 1.8→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1706 5 %RANDOM
Rwork0.177 ---
obs0.177 36728 99.8 %-
Displacement parametersBiso mean: 24.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2269 0 47 308 2624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.75
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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