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- PDB-4p69: Acek (D477A) ICDH complex -

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Basic information

Entry
Database: PDB / ID: 4p69
TitleAcek (D477A) ICDH complex
Components
  • Isocitrate dehydrogenase [NADP]
  • Isocitrate dehydrogenase kinase/phosphatase
KeywordsTRANSFERASE / HYDROLASE/OXIDOREDUCTASE / HYDROLASE-OXIDOREDUCTASE complex
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 / tricarboxylic acid cycle / electron transport chain ...[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 / tricarboxylic acid cycle / electron transport chain / 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 / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. ...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 / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / Isocitrate dehydrogenase [NADP] / Isocitrate dehydrogenase kinase/phosphatase
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsJimin, Z. / Nan, W. / Shu, W. / Zongchao, J.
CitationJournal: Chem. Commun. (Camb.) / Year: 2014
Title: The phosphatase mechanism of bifunctional kinase/phosphatase AceK.
Authors: Wang, S. / Shen, Q. / Chen, G. / Zheng, J. / Tan, H. / Jia, Z.
History
DepositionMar 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _citation.country / _diffrn_source.pdbx_synchrotron_site ..._citation.country / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 30, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_validate_close_contact / struct_conn
Item: _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)225,8988
Polymers224,3494
Non-polymers1,5494
Water37821
1
B: Isocitrate dehydrogenase kinase/phosphatase
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
hetero molecules

A: Isocitrate dehydrogenase kinase/phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,8988
Polymers224,3494
Non-polymers1,5494
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area16060 Å2
ΔGint-94 kcal/mol
Surface area80090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.160, 198.160, 156.071
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Detailsbiological unit is the same as asym.

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Components

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


Mass: 66495.984 Da / Num. of mol.: 2 / Fragment: residues 4-571 / Mutation: D477A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: aceK, Z5602, ECs4934 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): DE3
References: UniProt: Q8X607, [isocitrate dehydrogenase (NADP+)] kinase, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Protein Isocitrate dehydrogenase [NADP] / IDH / IDP / NADP(+)-specific ICDH / Oxalosuccinate decarboxylase


Mass: 45678.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: icd, icdA, icdE, b1136, JW1122 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): DE3
References: UniProt: P08200, isocitrate dehydrogenase (NADP+)
#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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: 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: 3.95 Å3/Da / Density % sol: 68.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2mM DTT, 10% glycerol, 0.1M MES pH 6.0, 25%~30% PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→19.96 Å / Num. obs: 27331 / % possible obs: 99 % / Redundancy: 13.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.044 / Net I/σ(I): 14.5 / Num. measured all: 367390 / Scaling rejects: 446
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.3-3.580.912.63426442910.5520.32298.5
9.9-19.96180.041451808610040.9990.0187.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Aimless0.1.27data scaling
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
RefinementResolution: 3.3→29.97 Å / WRfactor Rfree: 0.2338 / WRfactor Rwork: 0.1716 / FOM work R set: 0.8291 / SU B: 20.11 / SU ML: 0.337 / SU Rfree: 2.0802 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 2.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 414 4.8 %RANDOM
Rwork0.1767 8272 --
obs0.1803 -99.2188 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 193.58 Å2 / Biso mean: 81.787 Å2 / Biso min: 42.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.95 Å20 Å2
2---0.95 Å20 Å2
3---3.08 Å2
Refinement stepCycle: final / Resolution: 3.3→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15634 0 100 21 15755
Biso mean--76.9 71.29 -
Num. residues----1945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01916115
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215362
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.96721844
X-RAY DIFFRACTIONr_angle_other_deg0.917335303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8751938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1723.577780
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.974152760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.46415125
X-RAY DIFFRACTIONr_chiral_restr0.0870.22358
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118108
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023789
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 23 -
Rwork0.377 414 -
all-437 -
obs--11.45 %

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