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- PDB-6k5l: The crystal structure of isocitrate dehydrogenase kinase/phosphat... -

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Basic information

Entry
Database: PDB / ID: 6k5l
TitleThe crystal structure of isocitrate dehydrogenase kinase/phosphatase wtih two Mn2+ from E. coli
ComponentsIsocitrate dehydrogenase kinase/phosphatase
KeywordsHYDROLASE / kinase / phosphatase
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 / protein serine/threonine phosphatase activity / AMP binding / phosphoprotein phosphatase activity / tricarboxylic acid cycle / glucose metabolic process / manganese ion binding ...[isocitrate dehydrogenase (NADP+)] kinase / [isocitrate dehydrogenase (NADP+)] kinase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / glyoxylate cycle / protein serine/threonine phosphatase activity / AMP binding / phosphoprotein phosphatase activity / tricarboxylic acid cycle / glucose metabolic process / manganese ion binding / protein serine/threonine kinase activity / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Isocitrate dehydrogenase kinasephosphatase / Isocitrate dehydrogenase kinase/phosphatase (AceK), regulatory domain / Isocitrate dehydrogenase kinase/phosphatase (AceK), kinase domain / Isocitrate dehydrogenase kinase/phosphatase (AceK) kinase domain / Isocitrate dehydrogenase kinase/phosphatase (AceK), regulatory domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / : / Isocitrate dehydrogenase kinase/phosphatase / Isocitrate dehydrogenase kinase/phosphatase
Similarity search - Component
Biological speciesEscherichia coli O157 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZhang, X. / Lei, Z. / Zheng, J. / Jia, Z.
Funding support China, Canada, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21773014 China
Natural Sciences and Engineering Research Council (Canada)RGPIN-2018-04427 Canada
CitationJournal: Sci Rep / Year: 2019
Title: Characterization of metal binding of bifunctional kinase/phosphatase AceK and implication in activity modulation.
Authors: Zhang, X. / Shen, Q. / Lei, Z. / Wang, Q. / Zheng, J. / Jia, Z.
History
DepositionMay 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,41610
Polymers135,6472
Non-polymers1,7698
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-26 kcal/mol
Surface area49040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.484, 124.484, 266.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Isocitrate dehydrogenase 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 O157 (bacteria) / Gene: aceK / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1Z3UWE5, UniProt: P11071*PLUS, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.81 Å3/Da / Density % sol: 67.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6.5, 4% PEG8000, 15% Glycerol, 2mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 100893 / % possible obs: 97 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.09514 / Rrim(I) all: 0.1018 / Net I/σ(I): 23
Reflection shellResolution: 2.55→2.59 Å / Num. unique obs: 4784 / CC1/2: 0.598 / Rpim(I) all: 0.559

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LCB

3lcb


Resolution: 2.55→29.476 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.13
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.221 3045 3.02 %
Rwork0.1917 --
obs0.1926 69363 77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→29.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9251 0 104 172 9527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089609
X-RAY DIFFRACTIONf_angle_d1.04713038
X-RAY DIFFRACTIONf_dihedral_angle_d14.445698
X-RAY DIFFRACTIONf_chiral_restr0.0521378
X-RAY DIFFRACTIONf_plane_restr0.0061679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5469-2.58670.2846420.27331335X-RAY DIFFRACTION23
2.5867-2.6290.3112730.28982375X-RAY DIFFRACTION41
2.629-2.67430.3224880.29472837X-RAY DIFFRACTION49
2.6743-2.72290.3494910.27682943X-RAY DIFFRACTION51
2.7229-2.77530.3035930.27553016X-RAY DIFFRACTION52
2.7753-2.83190.3456960.2773061X-RAY DIFFRACTION53
2.8319-2.89340.2557920.27213086X-RAY DIFFRACTION54
2.8934-2.96070.31131000.26193267X-RAY DIFFRACTION56
2.9607-3.03460.2351120.23743624X-RAY DIFFRACTION63
3.0346-3.11660.26471330.21874177X-RAY DIFFRACTION73
3.1166-3.20820.26961590.22314963X-RAY DIFFRACTION86
3.2082-3.31160.28931720.22485512X-RAY DIFFRACTION97
3.3116-3.42980.22721860.20295773X-RAY DIFFRACTION100
3.4298-3.56690.21121780.19185819X-RAY DIFFRACTION100
3.5669-3.72890.18711830.18115746X-RAY DIFFRACTION100
3.7289-3.92510.23051830.1725791X-RAY DIFFRACTION100
3.9251-4.17040.20951750.1665756X-RAY DIFFRACTION100
4.1704-4.49140.16091780.14275752X-RAY DIFFRACTION100
4.4914-4.94140.16021760.14885797X-RAY DIFFRACTION100
4.9414-5.65210.22811740.17015778X-RAY DIFFRACTION100
5.6521-7.10450.21741750.20565761X-RAY DIFFRACTION100
7.1045-29.47790.1911860.17955679X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.19370.1607-0.06740.1753-0.13120.14480.18580.00110.06980.1035-0.0164-0.0399-0.1352-0.04650.20620.31850.01860.05430.27450.07780.239751.65725.30537.6878
20.33360.23110.31930.21020.17350.350.16110.09960.0261-0.04320.04080.03430.0786-0.08420.27550.32690.04440.05450.32540.13590.155738.40446.3435-2.7687
30.28780.1839-0.28350.3973-0.34570.3341-0.0420.1017-0.0403-0.2488-0.0744-0.14330.1088-0.0383-0.0520.32330.06460.04790.22080.01850.276358.8917-16.58333.142
40.37750.0378-0.03250.6064-0.32610.41680.04040.0972-0.03050.15610.13990.07230.0011-0.00240.48870.2514-0.0421-0.01990.1330.05890.199837.1591-16.691621.4374
50.4337-0.0314-0.06980.00840.00780.0111-0.0898-0.136-0.21930.09750.29680.0178-0.06730.0435-0.03850.5509-0.1291-0.17050.39520.09360.310745.8755-22.285244.4617
60.0827-0.0188-0.06710.0358-0.02240.09160.1079-0.2533-0.14740.2024-0.1625-0.34830.18440.3389-0.00030.4713-0.0264-0.13780.32960.06680.424460.8168-23.883329.0767
70.7101-0.01010.37410.5791-0.42430.4128-0.2466-0.14060.03690.0360.184-0.1745-0.0941-0.07710.04520.3562-0.0072-0.01710.2410.04090.301752.69848.881661.4442
80.5741-0.1617-0.04070.6765-0.00280.4194-0.0542-0.3296-0.0782-0.19060.1737-0.0069-0.0593-0.06110.30960.26830.04920.02510.18770.11580.299129.037612.615649.0713
90.14560.11930.02020.1084-0.04830.19530.09280.06250.0253-0.1182-0.0428-0.1906-0.11350.00830.03760.3750.05460.12290.15890.06250.345241.897415.989431.5519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 69 )
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 110 )
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 307 )
4X-RAY DIFFRACTION4chain 'A' and (resid 308 through 484 )
5X-RAY DIFFRACTION5chain 'A' and (resid 485 through 528 )
6X-RAY DIFFRACTION6chain 'A' and (resid 529 through 574 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 307 )
8X-RAY DIFFRACTION8chain 'B' and (resid 308 through 451 )
9X-RAY DIFFRACTION9chain 'B' and (resid 452 through 574 )

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