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- PDB-1fwk: CRYSTAL STRUCTURE OF HOMOSERINE KINASE COMPLEXED WITH ADP -

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Basic information

Entry
Database: PDB / ID: 1fwk
TitleCRYSTAL STRUCTURE OF HOMOSERINE KINASE COMPLEXED WITH ADP
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 / Homoserine kinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / Resolution: 2.1 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 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)130,9319
Polymers129,1974
Non-polymers1,7335
Water10,737596
1
A: HOMOSERINE KINASE
B: HOMOSERINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4534
Polymers64,5992
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-39 kcal/mol
Surface area23840 Å2
MethodPISA
2
C: HOMOSERINE KINASE
D: HOMOSERINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4775
Polymers64,5992
Non-polymers8793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-48 kcal/mol
Surface area23190 Å2
MethodPISA
3
C: HOMOSERINE KINASE
D: HOMOSERINE KINASE
hetero molecules

A: HOMOSERINE KINASE
B: HOMOSERINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9319
Polymers129,1974
Non-polymers1,7335
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
Buried area10350 Å2
ΔGint-88 kcal/mol
Surface area45530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.206, 129.147, 109.773
Angle α, β, γ (deg.)90.00, 105.52, 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 in the asymmeric unit.

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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: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 596 / 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: 3.29 Å3/Da / Density % sol: 62.58 %
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: Jul 4, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 97265 / Num. obs: 96677 / % possible obs: 99.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 29.5
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.026 / Num. unique all: 4826 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 316441
Reflection shell
*PLUS
% possible obs: 99.5 % / Mean I/σ(I) obs: 2.65

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Hube
RfactorNum. reflection% reflectionSelection details
Rfree0.246 4832 -RANDOM
Rwork0.209 ---
all-97265 --
obs-96677 99.4 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9076 0 109 596 9781
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.013
X-RAY DIFFRACTIONc_angle_d1.69
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.013

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