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- PDB-3eps: The crystal structure of isocitrate dehydrogenase kinase/phosphat... -

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Basic information

Entry
Database: PDB / ID: 3eps
TitleThe crystal structure of isocitrate dehydrogenase kinase/phosphatase from E. coli
ComponentsIsocitrate dehydrogenase kinase/phosphatase
Keywordstransferase / hydrolase / kinase phosphatase / ATP-binding / Glyoxylate bypass / Kinase / Nucleotide-binding / Protein phosphatase / Tricarboxylic acid cycle / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


[isocitrate dehydrogenase (NADP+)] kinase / [isocitrate dehydrogenase (NADP+)] kinase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / glyoxylate cycle / phosphoprotein phosphatase activity / tricarboxylic acid cycle / glucose metabolic process / phosphorylation / protein serine/threonine kinase activity / ATP binding / cytoplasm
Similarity search - Function
Isocitrate dehydrogenase kinase/phosphatase (AceK), regulatory domain / Isocitrate dehydrogenase kinase/phosphatase (AceK), kinase domain / Isocitrate dehydrogenase kinase/phosphatase (AceK), regulatory domain / Isocitrate dehydrogenase kinasephosphatase / Isocitrate dehydrogenase kinase/phosphatase (AceK) kinase domain
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Isocitrate dehydrogenase kinase/phosphatase
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsZheng, J. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Nature / Year: 2010
Title: Structure of the bifunctional isocitrate dehydrogenase kinase/phosphatase.
Authors: Zheng, J. / Jia, Z.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Isocitrate dehydrogenase kinase/phosphatase
B: Isocitrate dehydrogenase kinase/phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,3168
Polymers135,5592
Non-polymers1,7576
Water90150
1
A: Isocitrate dehydrogenase kinase/phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6584
Polymers67,7791
Non-polymers8793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isocitrate dehydrogenase kinase/phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6584
Polymers67,7791
Non-polymers8793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.595, 124.595, 267.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a monomer

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Components

#1: Protein Isocitrate dehydrogenase kinase/phosphatase / IDH kinase/phosphatase / IDHK/P


Mass: 67779.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: K-12 / Gene: aceK, ECs4934, Z5602 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: Q8X607, [isocitrate dehydrogenase (NADP+)] kinase, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.83 Å3/Da / Density % sol: 67.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG8000, 0.2M magnesium chloride, 0.1M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.919 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 52700 / Num. obs: 45600 / % possible obs: 86.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 73.8 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 305.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.4 / % possible all: 96.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→30 Å
RfactorNum. reflection% reflection
Rfree0.268 43301 -
Rwork0.233 --
obs0.233 45600 86.5 %
all-52700 -
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9307 0 110 50 9467

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