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- PDB-6pay: Structure of HsICDH1:Mg(II):ICT:NADPH(50%) complex reveals struct... -

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Basic information

Entry
Database: PDB / ID: 6pay
TitleStructure of HsICDH1:Mg(II):ICT:NADPH(50%) complex reveals structural basis for observation of half-sites reactivity
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE / substrate complex / half-sites reactivity / ICDH mechanism
Function / homology
Function and homology information


Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / peroxisomal matrix / tricarboxylic acid cycle / glutathione metabolic process / Peroxisomal protein import / peroxisome / NAD binding / tertiary granule lumen / NADP binding / secretory granule lumen / ficolin-1-rich granule lumen / response to oxidative stress / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / 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
FORMIC ACID / ISOCITRIC ACID / Chem-NDP / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsSilvaggi, N.R. / Melkonian, T.R. / Roman, J.V. / Moran, G.R.
CitationJournal: Biochemistry / Year: 2019
Title: Transient-State Analysis of Human Isocitrate Dehydrogenase I: Accounting for the Interconversion of Active and Non-Active Conformational States.
Authors: Roman, J.V. / Melkonian, T.R. / Silvaggi, N.R. / Moran, G.R.
History
DepositionJun 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.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_conn.ptnr2_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 [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
C: Isocitrate dehydrogenase [NADP] cytoplasmic
D: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,81420
Polymers186,8814
Non-polymers1,93316
Water6,503361
1
A: Isocitrate dehydrogenase [NADP] cytoplasmic
D: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,84912
Polymers93,4402
Non-polymers1,40810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-66 kcal/mol
Surface area30360 Å2
MethodPISA
2
B: Isocitrate dehydrogenase [NADP] cytoplasmic
C: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9658
Polymers93,4402
Non-polymers5256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-67 kcal/mol
Surface area31450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.600, 74.600, 142.900
Angle α, β, γ (deg.)90.00, 95.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Isocitrate dehydrogenase [NADP] cytoplasmic / IDH / Cytosolic NADP-isocitrate dehydrogenase / IDP / NADP(+)-specific ICDH / Oxalosuccinate ...IDH / Cytosolic NADP-isocitrate dehydrogenase / IDP / NADP(+)-specific ICDH / Oxalosuccinate decarboxylase / Isocitrate dehydrogenase 1


Mass: 46720.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH1, PICD / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O75874, isocitrate dehydrogenase (NADP+)

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Non-polymers , 5 types, 377 molecules

#2: Chemical
ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.69 Å3/Da / Density % sol: 54.3 % / Description: Thick plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 20% PEG3350, 10% Tacsimate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.199→47.105 Å / Num. obs: 100492 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.033 / Rrim(I) all: 0.064 / Net I/σ(I): 12.7
Reflection shellResolution: 2.199→2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6030 / CC1/2: 0.903 / Rpim(I) all: 0.271 / Rrim(I) all: 0.522 / % possible all: 89.6

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Processing

Software
NameVersionClassification
PHENIX(dev_3525: ???)refinement
HKL-2000v715data reduction
HKL-2000v715data scaling
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1T0L

1t0l


Resolution: 2.199→47.105 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 1898 2.2 %
Rwork0.2242 --
obs0.2246 86426 85.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.199→47.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12757 0 117 361 13235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313133
X-RAY DIFFRACTIONf_angle_d0.58117750
X-RAY DIFFRACTIONf_dihedral_angle_d13.3857767
X-RAY DIFFRACTIONf_chiral_restr0.0441929
X-RAY DIFFRACTIONf_plane_restr0.0032281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1986-2.25360.3064820.28513600X-RAY DIFFRACTION51
2.2536-2.31460.3051870.29034240X-RAY DIFFRACTION60
2.3146-2.38270.34391090.29164640X-RAY DIFFRACTION66
2.3827-2.45960.28811140.28725065X-RAY DIFFRACTION72
2.4596-2.54750.27721240.27725528X-RAY DIFFRACTION78
2.5475-2.64950.33211420.28356058X-RAY DIFFRACTION86
2.6495-2.770.29721420.26876582X-RAY DIFFRACTION93
2.77-2.9160.27541490.26716650X-RAY DIFFRACTION95
2.916-3.09870.27971520.25726852X-RAY DIFFRACTION97
3.0987-3.33790.22691560.23616931X-RAY DIFFRACTION98
3.3379-3.67370.2461600.21557000X-RAY DIFFRACTION99
3.6737-4.2050.18911590.18847084X-RAY DIFFRACTION100
4.205-5.29670.17931610.16487123X-RAY DIFFRACTION100
5.2967-47.11610.23141610.19277175X-RAY DIFFRACTION99
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)
11.12740.30060.97170.8632-0.20341.1533-0.0902-0.53770.32340.33390.2967-0.28-0.13580.3859-0.08130.31490.0564-0.01360.6188-0.26080.3719-23.9346.1188-9.354
20.67890.3331-0.22940.4410.23140.4843-0.11250.10230.3374-0.18360.1575-0.1302-0.14570.2904-0.05890.2604-0.2160.06120.3965-0.12790.3966-25.28896.5365-30.8839
30.013-0.0103-0.01960.06630.04070.0775-0.0020.05530.194-0.23040.0992-0.1413-0.19370.04880.02220.2691-0.52280.1870.3069-0.05870.6154-23.577110.974-40.1033
40.03160.0170.07260.03070.04290.18930.00910.14520.2945-0.16580.0232-0.3954-0.06750.22260.10270.4546-0.36410.21680.5166-0.09320.5327-10.68192.7615-43.3634
50.31-0.14420.14061.0750.0821.5396-0.2574-0.46620.11570.2160.3737-0.31150.15540.5326-0.10010.19850.02130.01010.6444-0.18410.3764-14.0759-5.1451-18.226
65.24282.52211.02292.40070.12290.55980.1565-0.3656-0.49580.3404-0.0216-0.6090.03180.3888-0.12080.50180.32-0.10621.2272-0.1210.4776-4.9784-9.6989-5.2291
74.35981.00751.07082.09130.26941.4921-0.0870.5550.0433-0.13030.13850.035-0.486-0.0231-0.04350.34180.07210.00930.3011-0.00420.1414-23.07685.49288.4631
80.4767-0.3638-0.03460.7369-0.07190.5478-0.195-0.07660.14020.36960.1711-0.025-0.5814-0.0528-0.02130.51810.5423-0.01380.1776-0.06160.319-27.19415.361933.8889
92.22720.41090.18442.6464-0.12541.56280.08320.4391-0.2433-0.3012-0.01090.09520.1161-0.3841-0.06840.30760.0529-0.02640.3662-0.03980.1893-35.8664-9.45299.3344
103.04071.4765-1.30042.11090.60711.67440.174-0.86310.21040.7416-0.2265-0.0802-0.3009-0.17320.04340.70470.1177-0.12010.6106-0.10250.2932-16.1571-7.340763.4597
111.7911-0.12490.40770.51350.17230.3770.0042-0.1285-0.31170.17280.0558-0.0950.14340.0314-0.07690.43060.184-0.0280.2475-0.00930.3055-18.6602-15.408344.015
120.6816-0.8125-0.30991.9493-0.53920.9723-0.3534-0.11850.48210.26430.1787-0.4624-0.46590.10120.13750.82530.069-0.280.2976-0.12740.524-6.431513.081940.1861
130.8832-0.0456-0.14971.4486-0.0441.0049-0.1647-0.014-0.05280.05950.1541-0.2486-0.16380.28830.01820.34790.2015-0.06570.2892-0.10230.3426-8.0451-6.770332.2546
140.8782-0.51740.05740.6038-0.22010.1276-0.1489-0.3131-0.13320.37430.1247-0.12370.00640.00570.03670.45880.3389-0.04240.2595-0.01830.3248-17.4675-12.91444.1668
152.18830.5519-0.34890.60190.052.24540.0386-0.9147-0.34580.5521-0.1324-0.21590.4365-0.27930.09280.66030.0488-0.06560.49670.08940.3705-25.9977-23.814458.2999
162.1407-0.90770.50011.42130.69081.18380.16410.8112-0.0478-0.809-0.19830.0961-0.1979-0.04010.04740.9231-0.2244-0.08670.8686-0.02170.3137-34.4166-7.7734-62.8285
171.18350.06370.12110.2118-0.37890.75870.00590.27530.083-0.42830.1303-0.04030.05080.016-0.13530.4008-0.17930.00680.2827-0.02410.2579-35.3087-2.6258-41.6962
181.114-0.07550.05070.90950.27610.4455-0.09930.1664-0.1308-0.32770.14090.24080.1035-0.0231-0.03030.344-0.24350.00880.2825-0.00850.3274-36.7677-8.3391-35.191
190.3461-0.19490.16690.1314-0.22020.77220.06630.2823-0.1833-0.3728-0.0350.05880.09950.3726-0.09590.9387-0.27420.05410.8394-0.39380.4645-24.0986-23.6127-58.3134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 234 )
4X-RAY DIFFRACTION4chain 'A' and (resid 235 through 260 )
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 393 )
6X-RAY DIFFRACTION6chain 'A' and (resid 394 through 412 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 94 )
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 312 )
9X-RAY DIFFRACTION9chain 'B' and (resid 313 through 413 )
10X-RAY DIFFRACTION10chain 'C' and (resid 5 through 94 )
11X-RAY DIFFRACTION11chain 'C' and (resid 95 through 133 )
12X-RAY DIFFRACTION12chain 'C' and (resid 134 through 164 )
13X-RAY DIFFRACTION13chain 'C' and (resid 165 through 260 )
14X-RAY DIFFRACTION14chain 'C' and (resid 261 through 311 )
15X-RAY DIFFRACTION15chain 'C' and (resid 312 through 412 )
16X-RAY DIFFRACTION16chain 'D' and (resid 5 through 94 )
17X-RAY DIFFRACTION17chain 'D' and (resid 95 through 164 )
18X-RAY DIFFRACTION18chain 'D' and (resid 165 through 311 )
19X-RAY DIFFRACTION19chain 'D' and (resid 312 through 412 )

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