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- PDB-6g3u: Structure of Pseudomonas aeruginosa Isocitrate Dehydrogenase, IDH -

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Basic information

Entry
Database: PDB / ID: 6g3u
TitleStructure of Pseudomonas aeruginosa Isocitrate Dehydrogenase, IDH
ComponentsIsocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / Isocitrate dehydrogenase / TCA cycle / metabolism / Pseudomonas aeruginosa
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / nucleotide binding / metal ion binding
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, monomeric / Monomeric isocitrate dehydrogenase
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.707 Å
AuthorsCrousilles, A. / Welch, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Gluconeogenic precursor availability regulates flux through the glyoxylate shunt inPseudomonas aeruginosa.
Authors: Crousilles, A. / Dolan, S.K. / Brear, P. / Chirgadze, D.Y. / Welch, M.
History
DepositionMar 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isocitrate dehydrogenase
B: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,3884
Polymers162,4992
Non-polymers8902
Water3,549197
1
A: Isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1393
Polymers81,2491
Non-polymers8902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isocitrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)81,2491
Polymers81,2491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.460, 149.020, 201.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 593 or (resid 600...
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEU(chain A and (resid 5 through 593 or (resid 600...AA5 - 5931 - 589
12ARGARGARGARG(chain A and (resid 5 through 593 or (resid 600...AA600596
13SERSERALAALA(chain A and (resid 5 through 593 or (resid 600...AA5 - 7411 - 737
21SERSERLEULEUchain BBB5 - 7401 - 736

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Components

#1: Protein Isocitrate dehydrogenase


Mass: 81249.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: idh, PA2624 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q9I0L4
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, Sodium phosphate monobasic, glycerol, NADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.7→29.62 Å / Num. obs: 51799 / % possible obs: 98 % / Redundancy: 18.2 % / Biso Wilson estimate: 43.36 Å2 / Rrim(I) all: 0.176 / Net I/σ(I): 19
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3682 / Rrim(I) all: 0.891 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZDA

4zda


Resolution: 2.707→29.618 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.05
RfactorNum. reflection% reflection
Rfree0.2668 2630 5.08 %
Rwork0.2076 --
obs0.2106 51765 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.42 Å2 / Biso mean: 52.3057 Å2 / Biso min: 10.02 Å2
Refinement stepCycle: final / Resolution: 2.707→29.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11296 0 58 197 11551
Biso mean--28.88 35.87 -
Num. residues----1467
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4426X-RAY DIFFRACTION13.23TORSIONAL
12B4426X-RAY DIFFRACTION13.23TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7075-2.75670.3491280.2722455258396
2.7567-2.80970.32361440.246325682712100
2.8097-2.8670.32731330.257426042737100
2.867-2.92930.31461370.254525122649100
2.9293-2.99730.34611330.251625762709100
2.9973-3.07220.34291340.240825902724100
3.0722-3.15520.29251350.23992570270599
3.1552-3.24790.31641240.235525732697100
3.2479-3.35260.311600.227625452705100
3.3526-3.47230.29351570.230225532710100
3.4723-3.61110.26741520.209825702722100
3.6111-3.77510.27161180.203426062724100
3.7751-3.97370.25921350.195725902725100
3.9737-4.2220.24561460.179226092755100
4.222-4.54690.21241230.16525962719100
4.5469-5.00250.2141340.166226102744100
5.0025-5.72190.25211460.183726382784100
5.7219-7.19190.24231450.22426322777100
7.1919-29.61950.22781460.202227382884100

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