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- PDB-1tyo: Isocitrate Dehydrogenase from the hyperthermophile Aeropyrum pern... -

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Basic information

Entry
Database: PDB / ID: 1tyo
TitleIsocitrate Dehydrogenase from the hyperthermophile Aeropyrum pernix in complex with etheno-NADP
Componentsisocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / Enzyme-ethenoNADP complex
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / NAD binding / magnesium ion binding
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / 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
ETHENO-NADP / isocitrate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKarlstrom, M. / Stokke, R. / Steen, I.H. / Birkeland, N. / Ladenstein, R.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability
Authors: Karlstrom, M. / Stokke, R. / Steen, I.H. / Birkeland, N.K. / Ladenstein, R.
History
DepositionJul 8, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3May 23, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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
B: isocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6293
Polymers95,9662
Non-polymers6631
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-39 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.007, 107.007, 179.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEARGARG2AA125 - 257125 - 257
21ILEILEARGARG2BB125 - 257125 - 257
32ILEILEVALVAL2AA279 - 321279 - 321
42ILEILEVALVAL2BB279 - 321279 - 321
53SERSERALAALA6AA6 - 1246 - 124
63PROPROALAALA6BB7 - 1247 - 124
74GLYGLYLEULEU6AA322 - 430322 - 430
84GLYGLYLEULEU6BB322 - 430322 - 430

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Components

#1: Protein isocitrate dehydrogenase /


Mass: 47982.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)
References: UniProt: Q9YE81, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-ENP / ETHENO-NADP


Type: RNA linking / Mass: 663.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H24N5O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 6000, Magnesium chloride, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9089 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 24, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9089 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 57561 / Num. obs: 57512 / % possible obs: 100 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 2 / Redundancy: 19 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.6
Reflection shellResolution: 2.15→2.17 Å / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ICD

3icd


Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.824 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24936 2909 5.1 %RANDOM
Rwork0.2234 ---
all0.22579 57512 --
obs0.22471 54556 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.573 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6607 0 32 201 6840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216732
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9689152
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.21015
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025132
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.23245
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2309
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4231.54223
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71726788
X-RAY DIFFRACTIONr_scbond_it1.52732509
X-RAY DIFFRACTIONr_scangle_it2.1984.52364
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
704tight positional0.060.05
732medium positional0.450.5
1653loose positional0.755
704tight thermal0.140.5
732medium thermal0.912
1653loose thermal1.8810
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.244 226
Rwork0.23 3937
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)
11.9365-0.0277-0.13551.1992-0.03251.37980.0683-0.15140.04250.15890.0149-0.1283-0.1140.1388-0.08320.0997-0.03050.01770.0361-0.020.039-38.3111205.4165-281.094
21.2514-0.5423-0.10411.1509-0.28541.2992-0.04650.0388-0.1638-0.0406-0.05570.02920.1917-0.01970.10220.0779-0.02530.04380.0085-0.01040.0703-39.6153182.2661-298.3626
31.0593-0.2688-0.11340.9593-0.54431.76490.05740.11130.0406-0.01820.00630.1015-0.1216-0.1748-0.06370.06510.01210.03810.0387-0.00470.0446-50.0474207.7749-295.4881
44.27-0.83490.45072.4071-0.48572.38060.16670.7754-0.8857-0.6785-0.1625-0.17460.61230.1969-0.00420.59330.10660.0460.2713-0.20780.3439-30.8735168.5394-332.1672
50.5917-0.2361-0.26321.2661-0.74071.1629-0.03270.0418-0.0038-0.1168-0.1333-0.20380.04390.13610.1660.10440.01030.04780.07650.0180.1063-26.8661190.1607-313.3837
65.7894-0.42781.78671.6489-0.61362.58320.26630.5721-0.2877-0.5606-0.15270.2150.3796-0.1521-0.11360.4131-0.0032-0.09180.2361-0.06180.1258-44.9765180.8572-332.1744
70.3824-0.1068-0.330.3751-0.04880.63840.04230.0293-0.0390.036-0.00470.01170.0035-0.0269-0.03760.1568-0.01040.030.1359-0.00550.14-43.2635200.2189-291.6468
80.1377-0.11920.20820.7624-0.53090.8737-0.04320.0154-0.07-0.21470.0116-0.02510.1023-0.01910.03160.23220.02860.03220.18210.0140.2086-31.1421186.3399-316.2335
93.32689.76-11.0962-39.7725-9.11771.34460.0302-0.1915-1.34930.2617-0.181-1.63241.4362-0.44150.15070.162900.00120.166-0.00090.167-61.3733197.9951-278.9314
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1316 - 131
2X-RAY DIFFRACTION2AA132 - 321132 - 321
3X-RAY DIFFRACTION3AA322 - 432322 - 432
4X-RAY DIFFRACTION4BB7 - 1317 - 131
5X-RAY DIFFRACTION5BB132 - 321132 - 321
6X-RAY DIFFRACTION6BB322 - 430322 - 430
7X-RAY DIFFRACTION7AD1002 - 1132
8X-RAY DIFFRACTION8BE439 - 502
9X-RAY DIFFRACTION9AC1001

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