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

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Basic information

Entry
Database: PDB / ID: 3lcb
TitleThe crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli.
Components(Isocitrate dehydrogenase ...) x 2
KeywordsTRANSFERASE / HYDROLASE / KINASE PHOSPHATASE / GLYOXYLATE BYPASS / HYDROLASEPROTEIN PHOSPHATASE / TRICARBOXYLIC ACID CYCLE / Isocitrate
Function / homology
Function and homology information


[isocitrate dehydrogenase (NADP+)] kinase / [isocitrate dehydrogenase (NADP+)] kinase activity / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / glyoxylate cycle / guanosine tetraphosphate binding / phosphoprotein phosphatase activity / electron transport chain / tricarboxylic acid cycle ...[isocitrate dehydrogenase (NADP+)] kinase / [isocitrate dehydrogenase (NADP+)] kinase activity / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / glyoxylate cycle / guanosine tetraphosphate binding / phosphoprotein phosphatase activity / electron transport chain / tricarboxylic acid cycle / glucose metabolic process / NAD binding / response to oxidative stress / phosphorylation / protein serine/threonine kinase activity / magnesium ion binding / ATP binding / cytosol / 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 / Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase ...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 / Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Isocitrate dehydrogenase kinase/phosphatase / Isocitrate dehydrogenase [NADP] / Isocitrate dehydrogenase kinase/phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZheng, J. / Jia, Z.
CitationJournal: Nature / Year: 2010
Title: Structure of the bifunctional isocitrate dehydrogenase kinase/phosphatase.
Authors: Zheng, J. / Jia, Z.
History
DepositionJan 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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: Isocitrate dehydrogenase kinase/phosphatase
B: Isocitrate dehydrogenase kinase/phosphatase
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,02410
Polymers227,2664
Non-polymers1,7576
Water37821
1
A: Isocitrate dehydrogenase kinase/phosphatase
hetero molecules

D: Isocitrate dehydrogenase [NADP]


Theoretical massNumber of molelcules
Total (without water)114,5125
Polymers113,6332
Non-polymers8793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4400 Å2
ΔGint-30 kcal/mol
Surface area42960 Å2
MethodPISA
2
B: Isocitrate dehydrogenase kinase/phosphatase
C: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5125
Polymers113,6332
Non-polymers8793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-31 kcal/mol
Surface area43150 Å2
MethodPISA
3
A: Isocitrate dehydrogenase kinase/phosphatase
B: Isocitrate dehydrogenase kinase/phosphatase
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
hetero molecules

A: Isocitrate dehydrogenase kinase/phosphatase
B: Isocitrate dehydrogenase kinase/phosphatase
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
hetero molecules

A: Isocitrate dehydrogenase kinase/phosphatase
B: Isocitrate dehydrogenase kinase/phosphatase
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)687,07130
Polymers681,79912
Non-polymers5,27218
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area60790 Å2
ΔGint-323 kcal/mol
Surface area223700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.801, 196.801, 156.458
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Isocitrate dehydrogenase ... , 2 types, 4 molecules ABCD

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


Mass: 67823.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: aceK, ECH74115_5487 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: B5Z0A8, UniProt: Q8X607*PLUS, [isocitrate dehydrogenase (NADP+)] kinase, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Protein Isocitrate dehydrogenase [NADP] / IDH / Oxalosuccinate decarboxylase / NADP(+)-specific ICDH / IDP


Mass: 45809.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1136, icd, icdA, icdE, icdh, JW1122 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: P08200, isocitrate dehydrogenase (NADP+)

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Non-polymers , 4 types, 27 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.85 Å3/Da / Density % sol: 68.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG 300, 0.1M MES, 0.05M magnesium chloride, 0.002M DTT,10% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9879 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9879 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.698
11K, H, -L20.302
ReflectionResolution: 2.9→30 Å / Num. all: 75640 / Num. obs: 38980 / % possible obs: 99.3 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 21.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 14 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3863 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 1 / SU B: 35.864 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3778 5.1 %RANDOM
Rwork0.19 ---
obs0.192 -98.15 %-
Displacement parametersBiso max: 130.73 Å2 / Biso mean: 71.363 Å2 / Biso min: 33.53 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å20 Å20 Å2
2---3.82 Å20 Å2
3---7.65 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15640 0 110 21 15771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02216129
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.96721866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.38751938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9823.593782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.494152762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.85115125
X-RAY DIFFRACTIONr_chiral_restr0.0730.22358
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112316
X-RAY DIFFRACTIONr_mcbond_it0.7181.59686
X-RAY DIFFRACTIONr_mcangle_it1.294215631
X-RAY DIFFRACTIONr_scbond_it1.0236443
X-RAY DIFFRACTIONr_scangle_it1.7554.56235
X-RAY DIFFRACTIONr_rigid_bond_restr0.657315988
LS refinement shellResolution: 2.9→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 244 -
Rwork0.346 4986 -
all-5230 -
obs--92.94 %

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