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- PDB-2uxq: Isocitrate dehydrogenase from the psychrophilic bacterium Desulfo... -

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Basic information

Entry
Database: PDB / ID: 2uxq
TitleIsocitrate dehydrogenase from the psychrophilic bacterium Desulfotalea psychrophila: biochemical properties and crystal structure analysis
ComponentsISOCITRATE DEHYDROGENASE NATIVE
KeywordsOXIDOREDUCTASE / PSYCHROPHILIC / COLD ADAPTATION / THERMAL STABILITY / ISOCITRATE DEHYDROGENASE
Function / homology
Function and homology information


isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / tricarboxylic acid cycle / NAD binding / magnesium ion binding
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
DI(HYDROXYETHYL)ETHER / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesDESULFOTALEA PSYCHROPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFedoy, A.-E. / Yang, N. / Martinez, A. / Leiros, H.-K.S. / Steen, I.H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural and Functional Properties of Isocitrate Dehydrogenase from the Psychrophilic Bacterium Desulfotalea Psychrophila Reveal a Cold -Active Enzyme with an Unusual High Thermal
Authors: Fedoy, A.-E. / Yang, N. / Martinez, A. / Leiros, H.-K.S. / Steen, I.H.
History
DepositionMar 29, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_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_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_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 NATIVE
B: ISOCITRATE DEHYDROGENASE NATIVE
C: ISOCITRATE DEHYDROGENASE NATIVE
D: ISOCITRATE DEHYDROGENASE NATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,03330
Polymers182,5974
Non-polymers2,43626
Water33,9221883
1
A: ISOCITRATE DEHYDROGENASE NATIVE
B: ISOCITRATE DEHYDROGENASE NATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,58616
Polymers91,2982
Non-polymers1,28714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-57.3 kcal/mol
Surface area36940 Å2
MethodPQS
2
C: ISOCITRATE DEHYDROGENASE NATIVE
D: ISOCITRATE DEHYDROGENASE NATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,44714
Polymers91,2982
Non-polymers1,14912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-40 kcal/mol
Surface area36980 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.324, 73.279, 126.413
Angle α, β, γ (deg.)98.90, 98.98, 113.88
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ISOCITRATE DEHYDROGENASE NATIVE


Mass: 45649.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOTALEA PSYCHROPHILA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q6AQ66

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Non-polymers , 5 types, 1909 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1883 / 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: 2.6 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.4
Details: 100 MM TRIS/HCL BUFFER PH 7.4, 1.7-1.9 M AMMONIUM SULPHATE, 2% PEG 400, 60 MM MGSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.75→55 Å / Num. obs: 162467 / % possible obs: 86.3 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.9
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.6 / % possible all: 45.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LWD

1lwd


Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.009 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 3240 2 %RANDOM
Rwork0.146 ---
obs0.146 159104 86.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.07 Å2-0.01 Å2
2---0.02 Å20.05 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12799 0 146 1883 14828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02213162
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211947
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.96317779
X-RAY DIFFRACTIONr_angle_other_deg0.893327718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44151637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2224.35577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.806152263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6581570
X-RAY DIFFRACTIONr_chiral_restr0.1020.21954
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214572
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022660
X-RAY DIFFRACTIONr_nbd_refined0.2140.22707
X-RAY DIFFRACTIONr_nbd_other0.1850.212371
X-RAY DIFFRACTIONr_nbtor_refined0.1760.26390
X-RAY DIFFRACTIONr_nbtor_other0.0860.27064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.21438
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.221.510553
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.408213040
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.47436003
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2924.54739
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: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 129
Rwork0.22 5593

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