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- PDB-3mbc: Crystal structure of monomeric isocitrate dehydrogenase from Cory... -

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Basic information

Entry
Database: PDB / ID: 3mbc
TitleCrystal structure of monomeric isocitrate dehydrogenase from Corynebacterium glutamicum in complex with NADP
ComponentsIsocitrate dehydrogenase [NADP]
KeywordsOXIDOREDUCTASE / Holoenzyme / Apoenzyme / Open conformation / NADP / Glyoxylate bypass / Magnesium / Metal-binding / Tricarboxylic acid cycle
Function / homologyIsocitrate dehydrogenase NADP-dependent, monomeric / Monomeric isocitrate dehydrogenase / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP]
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSidhu, N.S. / Aich, S. / Sheldrick, G.M. / Delbaere, L.T.J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of a highly NADP+-specific isocitrate dehydrogenase.
Authors: Sidhu, N.S. / Delbaere, L.T. / Sheldrick, G.M.
#1: Journal: Proteins / Year: 2006
Title: Substrate-free structure of a monomeric NADP isocitrate dehydrogenase: an open conformation phylogenetic relationship of isocitrate dehydrogenase.
Authors: Imabayashi, F. / Aich, S. / Prasad, L. / Delbaere, L.T.
#2: Journal: Structure / Year: 2002
Title: Structure of the monomeric isocitrate dehydrogenase: evidence of a protein monomerization by a domain duplication.
Authors: Yasutake, Y. / Watanabe, S. / Yao, M. / Takada, Y. / Fukunaga, N. / Tanaka, I.
#3: Journal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of the monomeric isocitrate dehydrogenase in the presence of NADP+: insight into the cofactor recognition, catalysis, and evolution.
Authors: Yasutake, Y. / Watanabe, S. / Yao, M. / Takada, Y. / Fukunaga, N. / Tanaka, I.
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Sep 21, 2011Group: Structure summary
Revision 1.4Nov 2, 2011Group: Database references
Revision 1.5Sep 6, 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 / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,1265
Polymers160,3342
Non-polymers7923
Water14,340796
1
A: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9353
Polymers80,1671
Non-polymers7682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1912
Polymers80,1671
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.840, 52.730, 236.370
Angle α, β, γ (deg.)90.00, 103.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Isocitrate dehydrogenase [NADP] / IDH / Oxalosuccinate decarboxylase


Mass: 80167.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13032
References: UniProt: P50216, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 796 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 25% polyethylene glycol 2000 monomethyl ether, 0.2 M tris[hydroxymethyl]aminomethane-HCl buffer, 0.2 M MgCl2, and 10 mM NADP, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2008
RadiationMonochromator: Double crystal monochromator with indirectly cryo-cooled and sagittally focusing crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→19.74 Å / Num. all: 122536 / Num. obs: 119827 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.66 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.94
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.25 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.5 / % possible all: 85.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.42 Å
Translation2.5 Å19.42 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MacromolecularCrystallography Data Collection (MXDC)data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2b0t split into 2 domains: Domain I (residues 2-138, and 558-737) and Domain II (139-557).

2b0t


Resolution: 1.9→19.74 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.725 / SU ML: 0.105 / SU R Cruickshank DPI: 0.157 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22926 5992 5 %RANDOM
Rwork0.18938 ---
obs0.19137 113834 100 %-
all-122536 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.086 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å20.45 Å2
2---1.53 Å20 Å2
3----0.12 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11204 0 33 796 12033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211450
X-RAY DIFFRACTIONr_bond_other_d0.0010.027512
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.96615564
X-RAY DIFFRACTIONr_angle_other_deg0.824318458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13951474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07125.522527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.795151927
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9471560
X-RAY DIFFRACTIONr_chiral_restr0.0790.21787
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112945
X-RAY DIFFRACTIONr_gen_planes_other00.022120
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_it2.16327318
X-RAY DIFFRACTIONr_mcbond_other0.75622986
X-RAY DIFFRACTIONr_mcangle_it2.864311726
X-RAY DIFFRACTIONr_scbond_it2.81924132
X-RAY DIFFRACTIONr_scangle_it3.94733836
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 383 -
Rwork0.222 7266 -
obs--100 %
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)
10.8391-0.06250.2541.28190.38023.04630.0392-0.2948-0.10080.3625-0.0166-0.02140.1026-0.0624-0.02260.1214-0.0302-0.00640.19810.02180.198321.0076.59837.4413
21.45140.55940.11951.03210.1471.43040.1263-0.1686-0.07750.2169-0.0541-0.064-0.03710.1543-0.07220.0866-0.0107-0.01260.1522-0.01030.210352.19650.323625.3261
31.0913-0.32530.19412.246-0.04482.1050.02870.05990.0093-0.0157-0.03020.0755-0.1123-0.05310.00150.0117-0.01270.00830.10630.01640.183718.75514.312116.171
40.44770.260.51011.1376-1.00734.1054-0.05520.20110.02390.06350.0738-0.0339-0.00660.4157-0.01860.5580.00060.06520.5309-0.04250.185280.44423.810978.9216
50.6822-0.02320.25341.70410.27451.6138-0.01050.01710.0805-0.03150.03960.3236-0.0919-0.0767-0.02920.6583-0.00190.04110.39340.05190.260150.768114.903282.5334
61.30470.21990.41512.97340.73782.0305-0.0604-0.0877-0.02290.26480.1784-0.15850.150.244-0.11810.7020.05990.05440.5056-0.05960.137180.615622.8045101.6619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 138
2X-RAY DIFFRACTION2A139 - 557
3X-RAY DIFFRACTION3A558 - 736
4X-RAY DIFFRACTION4B2 - 138
5X-RAY DIFFRACTION5B139 - 557
6X-RAY DIFFRACTION6B558 - 736

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