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- PDB-1xkd: Ternary complex of Isocitrate dehydrogenase from the hyperthermop... -

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Basic information

Entry
Database: PDB / ID: 1xkd
TitleTernary complex of Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix
Componentsisocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / Enzyme / ternary complex / isocitrate / Ca2+ / NADP+
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
ISOCITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / isocitrate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKarlstrom, M. / Stokke, R. / Steen, I.H. / Birkeland, N.-K. / 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
DepositionSep 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 23, 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_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 / _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)97,9178
Polymers95,9662
Non-polymers1,9516
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-67 kcal/mol
Surface area31680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.575, 107.575, 171.045
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

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
11TYRTYRARGARG2AA141 - 257141 - 257
21TYRTYRARGARG2BB141 - 257141 - 257
32GLUGLULYSLYS5AA258 - 278258 - 278
42GLUGLULYSLYS5BB258 - 278258 - 278
53ILEILELEULEU2AA279 - 320279 - 320
63ILEILELEULEU2BB279 - 320279 - 320

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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) / Strain: K1 / Gene: BAA79665 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)
References: UniProt: Q9YE81, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-ICT / ISOCITRIC ACID / Isocitric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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 6K, 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: 1.089 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: 1.089 Å / Relative weight: 1
ReflectionResolution: 2.3→39.7 Å / Num. all: 45289 / Num. obs: 45223 / % possible obs: 99.9 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 2 / Redundancy: 8.3 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 25.42
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 5.53 / Num. unique all: 2259 / % 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 1XGV

1xgv


Resolution: 2.3→39.7 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.155 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 1.35 / ESU R: 0.348 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24822 2289 5.1 %RANDOM
Rwork0.2261 ---
obs0.22722 42860 99.79 %-
all-45149 --
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: 26.931 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6568 0 124 196 6888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216733
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9849160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9835840
X-RAY DIFFRACTIONr_chiral_restr0.0930.21013
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025111
X-RAY DIFFRACTIONr_nbd_refined0.2130.23398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2345
X-RAY DIFFRACTIONr_metal_ion_refined0.1850.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.219
X-RAY DIFFRACTIONr_mcbond_it0.541.54189
X-RAY DIFFRACTIONr_mcangle_it0.97726717
X-RAY DIFFRACTIONr_scbond_it1.66832544
X-RAY DIFFRACTIONr_scangle_it2.6044.52443
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
636tight positional0.090.05
734medium positional0.630.5
71loose positional1.185
636tight thermal0.330.5
734medium thermal0.972
71loose thermal2.4210
LS refinement shellResolution: 2.3→2.361 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 155
Rwork0.249 3123
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)
11.65830.26940.2512.25410.25852.31270.1227-0.3255-0.25810.5162-0.0518-0.2050.15470.1163-0.07090.13960.0196-0.04590.2108-0.00850.0967258.602993.428-137.8816
24.81470.78921.52783.8817-1.58823.166-0.24121.0970.1647-0.92870.27320.70240.2456-0.494-0.0320.4008-0.1897-0.28470.67730.10830.4467221.123886.6199-187.2629
33.02911.1999-1.35771.0702-0.1691.5273-0.5540.4898-0.5509-0.37720.181-0.18140.3126-0.24770.37290.2066-0.14130.12460.2711-0.1490.207244.375480.6404-172.057
46.47791.1984-1.30275.3623-0.22293.0036-0.27451.13911.0267-1.11370.46970.2542-0.3518-0.3913-0.19520.4443-0.1123-0.18730.58360.28770.3178233.961799.7435-187.7695
516.25130.6759-23.330653.0374-17.762682.9569-0.98262.317-1.4951-3.03810.9372-1.13592.3825-1.73990.04550.27080.0205-0.0140.2674-0.03340.2719261.955488.8955-158.2737
656.48515.85036.0234-16.950556.712721.96660.0204-0.9045-1.76982.0979-0.7235-0.89452.2962-0.02610.70310.25180.0101-0.00570.23760.02410.2445250.354186.8269-157.5835
70.65880.25950.15920.89950.69741.53750.0266-0.0531-0.07210.08480.00530.0031-0.070.0393-0.03180.1210.02390.01580.1268-0.03290.1453253.402296.9098-148.7598
81.92521.1428-0.90950.6222-0.17681.5643-0.27960.2137-0.3477-0.26040.0977-0.12750.2857-0.00580.1820.1856-0.07080.09290.2769-0.10130.2735243.445581.0272-168.6034
912.84853.76191.6964-1.29011.49142.59410.2914-0.22440.7040.11930.0880.65740.31750.1035-0.37950.25850.00110.00030.25900.2571221.291483.3233-169.4942
102.52371.489-0.54381.70230.05861.9411-0.03720.03850.19640.0088-0.11120.4114-0.1299-0.40180.14840.01310.04170.00550.1788-0.07070.1707235.982393.0048-157.2941
111.10310.4428-0.14751.82280.37192.84240.01120.00470.0793-0.10020.0933-0.0574-0.41380.2773-0.10450.0864-0.0120.00350.1305-0.07090.073260.9861104.874-152.6168
1234.3537-2.92963.1111.707-7.061315.61060.04841.6244-0.9954-0.7065-0.1808-0.80860.6423-0.22640.13240.28070.0567-0.00610.2953-0.00680.2617230.05297.7979-173.5059
1310.0484-1.15813.7931-2.54513.3641-1.98370.20430.5621-0.11420.6778-0.1390.02580.1291-0.3402-0.06540.2621-0.0223-0.01720.27060.0270.2714230.458692.2326-170.9696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 131
2X-RAY DIFFRACTION2B6 - 131
3X-RAY DIFFRACTION3B132 - 321
4X-RAY DIFFRACTION4B322 - 426
5X-RAY DIFFRACTION5A1001
6X-RAY DIFFRACTION6A1002
7X-RAY DIFFRACTION6A1006
8X-RAY DIFFRACTION6A1134 - 1137
9X-RAY DIFFRACTION7A1009 - 1131
10X-RAY DIFFRACTION7B1014 - 1020
11X-RAY DIFFRACTION8A1132 - 1133
12X-RAY DIFFRACTION8B1021 - 1062
13X-RAY DIFFRACTION9B1063 - 1069
14X-RAY DIFFRACTION10A132 - 321
15X-RAY DIFFRACTION11A322 - 435
16X-RAY DIFFRACTION12B1003
17X-RAY DIFFRACTION13B1004
18X-RAY DIFFRACTION13A1005
19X-RAY DIFFRACTION13A1007 - 1008
20X-RAY DIFFRACTION13B1005 - 1013

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