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- PDB-1h74: CRYSTAL STRUCTURE OF HOMOSERINE KINASE COMPLEXED WITH ILE -

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Basic information

Entry
Database: PDB / ID: 1h74
TitleCRYSTAL STRUCTURE OF HOMOSERINE KINASE COMPLEXED WITH ILE
ComponentsHOMOSERINE KINASE
KeywordsTRANSFERASE / KINASE
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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ISOLEUCINE / Homoserine kinase
Similarity search - Component
Biological speciesMETHANOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,64713
Polymers129,1974
Non-polymers2,4509
Water7,945441
1
A: HOMOSERINE KINASE
B: HOMOSERINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8367
Polymers64,5992
Non-polymers1,2375
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-51.43 kcal/mol
Surface area23230 Å2
MethodPISA
2
C: HOMOSERINE KINASE
D: HOMOSERINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8126
Polymers64,5992
Non-polymers1,2134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-40 kcal/mol
Surface area22980 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

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
HOMOSERINE KINASE / HK


Mass: 32299.371 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 450 molecules

#2: Chemical
ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#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.: 441 / 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: 3.26 Å3/Da / Density % sol: 62.21 %
Crystal growpH: 8 / Details: PEG4000, SODIUM ACETATE, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 131766 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.05 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 26.9

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Processing

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

1fwl


Resolution: 1.9→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 6521 5 %RANDOM
Rwork0.21 ---
obs0.21 131766 99.3 %-
Displacement parametersBiso mean: 50.65 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9076 0 153 441 9670
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.62
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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