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- PDB-4zda: Crystal structure of isocitrate dehydrogenase in complex with iso... -

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Basic information

Entry
Database: PDB / ID: 4zda
TitleCrystal structure of isocitrate dehydrogenase in complex with isocitrate and Mn from M. smegmatis
ComponentsIsocitrate dehydrogenase (NADP) Icd2
KeywordsOXIDOREDUCTASE / ICD / M. smegmatis / complex / Isocitrate
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, monomeric / Monomeric isocitrate dehydrogenase
Similarity search - Domain/homology
ISOCITRIC ACID / : / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPojer, F. / Murima, P. / McKinney, J.D.
CitationJournal: To Be Published
Title: crystal structure of isocitrate dehydrogenase in complex with isocitrate and Mn from M. smegmatis
Authors: Pojer, F. / Murima, P. / McKinney, J.D.
History
DepositionApr 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isocitrate dehydrogenase (NADP) Icd2
B: Isocitrate dehydrogenase (NADP) Icd2
C: Isocitrate dehydrogenase (NADP) Icd2
D: Isocitrate dehydrogenase (NADP) Icd2
E: Isocitrate dehydrogenase (NADP) Icd2
F: Isocitrate dehydrogenase (NADP) Icd2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,97018
Polymers513,4886
Non-polymers1,48212
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12680 Å2
ΔGint-2 kcal/mol
Surface area170440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.774, 206.162, 145.598
Angle α, β, γ (deg.)90.00, 90.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Isocitrate dehydrogenase (NADP) Icd2 / Isocitrate dehydrogenase / NADP-dependent


Mass: 85581.336 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: icd2, MSMEG_1654, MSMEI_1615 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QSZ3, isocitrate dehydrogenase (NADP+)
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.05 M MgCl2, 28-34% Polyethylene glycol monomethyl ether 550 (Qiagen), and 0.1M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 145405 / % possible obs: 97.4 % / Redundancy: 2.16 % / Net I/σ(I): 12.81

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.59 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.914 / SU B: 15.905 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 7271 5 %RANDOM
Rwork0.21393 ---
obs0.21611 138134 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.633 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.09 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.8→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34476 0 84 0 34560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0235241
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.97447648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.80154406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6124.6481549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.056156361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.10215198
X-RAY DIFFRACTIONr_chiral_restr0.0710.25317
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02126392
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.796→2.868 Å
RfactorNum. reflection% reflection
Rfree0.448 490 -
Rwork-9262 -
obs--91.37 %

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