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- PDB-6ajb: Crystal structure of Trypanosoma brucei glycosomal isocitrate deh... -

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Basic information

Entry
Database: PDB / ID: 6ajb
TitleCrystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADH, alpha-ketoglutarate and ca2+
ComponentsIsocitrate dehydrogenase [NADP]
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / glycosome / metabolism / isocitrate dehydrogenase
Function / homology
Function and homology information


isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP metabolic process / glycosome / tricarboxylic acid cycle / NAD binding / magnesium ion binding / mitochondrion
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
2-OXOGLUTARIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, X. / Inaoka, D.K. / Shiba, T. / Balogun, E.O. / Ziebart, N. / Allman, S. / Watanabe, Y. / Nozaki, T. / Boshart, M. / Bringaud, F. ...Wang, X. / Inaoka, D.K. / Shiba, T. / Balogun, E.O. / Ziebart, N. / Allman, S. / Watanabe, Y. / Nozaki, T. / Boshart, M. / Bringaud, F. / Harada, S. / Kita, K.
CitationJournal: To Be Published
Title: Biochemical characterization of a novel Trypanosoma brucei glycosomal isocitrate dehydrogenase with dual coenzyme specificity (NADP+/NAD+)
Authors: Wang, X. / Inaoka, D.K. / Shiba, T. / Balogun, E.O. / Ziebart, N. / Allman, S. / Watanabe, Y. / Nozaki, T. / Boshart, M. / Bringaud, F. / Harada, S. / Kita, K.
History
DepositionAug 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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]
B: Isocitrate dehydrogenase [NADP]
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,12613
Polymers187,1664
Non-polymers2,9609
Water0
1
A: Isocitrate dehydrogenase [NADP]
B: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9906
Polymers93,5832
Non-polymers1,4074
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-90 kcal/mol
Surface area33740 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1367
Polymers93,5832
Non-polymers1,5535
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-89 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.520, 70.464, 121.929
Angle α, β, γ (deg.)90.00, 113.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Isocitrate dehydrogenase [NADP]


Mass: 46791.590 Da / Num. of mol.: 4 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: ILtat 1.4 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli)
References: UniProt: Q387G0, isocitrate dehydrogenase (NADP+)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
Sequence detailsThe sequence was derived from Trypanosome brucei brucei ILtat 1.4. However, the sequence reference ...The sequence was derived from Trypanosome brucei brucei ILtat 1.4. However, the sequence reference available at uniprot at the time of data processing was derived from a different strain TRYPANOSOMA BRUCEI BRUCEI (STRAIN 927/4 GUTAT10.1) (taxonomy ID 185431).

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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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 6000, 100 mM HEPES/NaOH pH 7.0, 200mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 39505 / % possible obs: 93.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 5.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 1842 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AJ6

6aj6


Resolution: 2.9→19.98 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.839 / SU B: 57.731 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.569 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28356 1741 5.1 %RANDOM
Rwork0.19178 ---
obs0.19645 32695 81.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.642 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20.25 Å2
2---0.54 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.9→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13048 0 190 0 13238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01913521
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212829
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.96618293
X-RAY DIFFRACTIONr_angle_other_deg1.114329526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5251637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40423.499603
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.193152380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4181596
X-RAY DIFFRACTIONr_chiral_restr0.1040.22018
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215045
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023131
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7614.2416560
X-RAY DIFFRACTIONr_mcbond_other1.7614.246559
X-RAY DIFFRACTIONr_mcangle_it3.0256.3548193
X-RAY DIFFRACTIONr_mcangle_other3.0256.3558194
X-RAY DIFFRACTIONr_scbond_it1.6524.4086961
X-RAY DIFFRACTIONr_scbond_other1.6524.4086957
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8766.52810097
X-RAY DIFFRACTIONr_long_range_B_refined5.07333.26215330
X-RAY DIFFRACTIONr_long_range_B_other5.07433.2615328
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 40 -
Rwork0.323 765 -
obs--26.83 %
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)
10.29770.01350.27030.1249-0.18380.8702-0.18350.01980.0281-0.0290.0445-0.0243-0.0284-0.06140.1390.1497-0.03190.00290.1199-0.03220.072845.6604-15.17830.7158
20.0974-0.07870.15350.60490.33050.65370.0489-0.01810.0516-0.0031-0.0714-0.11280.0624-0.04570.02250.0547-0.08750.03990.1865-0.0630.10265.8138-38.158150.1878
30.2253-0.21160.37830.292-0.23950.80460.0375-0.1502-0.017-0.02620.1474-0.08490.1411-0.2646-0.18490.0623-0.091-0.05130.23230.02050.125126.003115.3187-1.6166
40.48840.21020.26870.3998-0.14750.4932-0.0939-0.0729-0.0143-0.09290.0519-0.14080.0076-0.26740.0420.0667-0.02180.00330.24760.0170.101213.587436.812-24.8563
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 501
2X-RAY DIFFRACTION2B1 - 501
3X-RAY DIFFRACTION3C7 - 501
4X-RAY DIFFRACTION4D1 - 501

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