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- PDB-3r8w: Structure of 3-isopropylmalate dehydrogenase isoform 2 from Arabi... -

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Basic information

Entry
Database: PDB / ID: 3r8w
TitleStructure of 3-isopropylmalate dehydrogenase isoform 2 from Arabidopsis thaliana at 2.2 angstrom resolution
Components3-isopropylmalate dehydrogenase 2, chloroplastic
KeywordsOXIDOREDUCTASE / dimer / isocitrate and isopropylmalate dehydrogenases family / leucine biosynthesis / glucosinolate biosynthesis / NADH / 3-isopropylmalate / chloroplast
Function / homology
Function and homology information


embryo sac development / 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / pollen development / L-leucine biosynthetic process / chloroplast envelope / plastid / chloroplast stroma / NAD+ binding / chloroplast ...embryo sac development / 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / pollen development / L-leucine biosynthetic process / chloroplast envelope / plastid / chloroplast stroma / NAD+ binding / chloroplast / magnesium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
Isopropylmalate dehydrogenase / 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
ACETATE ION / 3-isopropylmalate dehydrogenase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHe, Y. / Galant, A. / Pang, Q. / Strul, J.M. / Balogun, S. / Jez, J.M. / Chen, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and functional evolution of isopropylmalate dehydrogenases in the leucine and glucosinolate pathways of Arabidopsis thaliana.
Authors: He, Y. / Galant, A. / Pang, Q. / Strul, J.M. / Balogun, S.F. / Jez, J.M. / Chen, S.
History
DepositionMar 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 3-isopropylmalate dehydrogenase 2, chloroplastic
B: 3-isopropylmalate dehydrogenase 2, chloroplastic
C: 3-isopropylmalate dehydrogenase 2, chloroplastic
D: 3-isopropylmalate dehydrogenase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,56819
Polymers173,6834
Non-polymers88615
Water8,251458
1
A: 3-isopropylmalate dehydrogenase 2, chloroplastic
B: 3-isopropylmalate dehydrogenase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,49113
Polymers86,8412
Non-polymers64911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-33 kcal/mol
Surface area27210 Å2
MethodPISA
2
C: 3-isopropylmalate dehydrogenase 2, chloroplastic
D: 3-isopropylmalate dehydrogenase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0786
Polymers86,8412
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-30 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.812, 211.016, 76.903
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-isopropylmalate dehydrogenase 2, chloroplastic / / 3-IPM-DH 2 / IMDH 2 / Beta-IPM dehydrogenase 2


Mass: 43420.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g80560, IMDH, IMDH2, T21F11.11 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P93832, 3-isopropylmalate dehydrogenase
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.68
Details: 20% PEG 4000, 20% glycerol, 0.16M ammonium sulfate, 0.08 sodium acetate trihydrate , pH 4.68, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2010 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.25→37 Å / Num. obs: 114991 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.25→2.29 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→36.998 Å / SU ML: 0.34 / σ(F): 1 / Phase error: 22.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 5388 5.03 %Random
Rwork0.1754 ---
obs0.177 107153 92.81 %-
all-114991 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.623 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.691 Å2-0 Å20.1501 Å2
2---6.6372 Å2-0 Å2
3---3.9462 Å2
Refinement stepCycle: LAST / Resolution: 2.25→36.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10795 0 60 458 11313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711146
X-RAY DIFFRACTIONf_angle_d0.9815072
X-RAY DIFFRACTIONf_dihedral_angle_d12.3664170
X-RAY DIFFRACTIONf_chiral_restr0.0611729
X-RAY DIFFRACTIONf_plane_restr0.0042000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.33040.29974380.26348896X-RAY DIFFRACTION81
2.3304-2.42370.325170.25689037X-RAY DIFFRACTION83
2.4237-2.5340.28295120.21959680X-RAY DIFFRACTION89
2.534-2.66760.26415170.213610079X-RAY DIFFRACTION92
2.6676-2.83460.25275620.209210271X-RAY DIFFRACTION94
2.8346-3.05340.23545550.199610536X-RAY DIFFRACTION96
3.0534-3.36050.22475450.186210774X-RAY DIFFRACTION98
3.3605-3.84630.21085780.182110869X-RAY DIFFRACTION99
3.8463-4.84430.15725820.13410911X-RAY DIFFRACTION99
4.8443-37.0030.18915820.162510712X-RAY DIFFRACTION97
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)
13.84662.2509-1.05171.6655-0.7412.2208-0.21680.1488-0.3593-0.16260.27930.00340.2828-0.2377-0.03310.4007-0.04060.00450.27480.02690.45335.7303-24.549710.4072
20.7549-0.05210.06782.0151-0.22331.1164-0.0195-0.1074-0.18390.15160.1905-0.07040.0623-0.0737-0.15590.35560.03650.03710.43040.06020.417721.0714-8.580523.7445
32.01231.4514-1.13932.04430.81582.2709-0.2610.1848-0.6137-0.33170.3498-0.3490.13460.0357-0.01440.4504-0.02070.10510.3931-0.10760.518720.7118-22.42223.396
42.242-0.4821-0.74551.11782.03944.2315-0.0821-0.20750.24620.03070.32-0.1403-0.35130.234-0.2010.50340.02240.01920.3165-0.04090.453828.317424.359232.9277
51.1332-0.0855-0.05811.9737-0.10951.0806-0.1969-0.09570.0719-0.04580.2270.149-0.2048-0.062-0.02610.42050.06050.03150.41620.03680.341614.60298.353417.4402
61.41350.392-1.01421.92451.34122.3895-0.0317-0.01090.1363-0.37850.3707-0.4166-0.65040.2208-0.33850.5859-0.10570.11320.4215-0.03250.511335.218921.998617.5082
72.1880.44481.12541.14122.10994.4384-0.02070.2256-0.3265-0.00580.2513-0.20910.47440.1598-0.22180.4841-0.0197-0.02410.2782-0.04440.4399-9.9965-77.51925.5357
81.3426-0.04210.15832.2263-0.18150.8035-0.17470.1019-0.06830.02540.2080.14030.1941-0.0504-0.03960.3962-0.0608-0.03190.40610.02970.3261-23.7753-61.499220.9912
92.2603-0.91241.00652.07621.22832.0985-0.09170.0078-0.20740.30.3387-0.36130.61090.2134-0.28780.56210.1004-0.08740.4364-0.01370.4676-3.2721-75.25820.9349
104.1637-1.88880.76851.0085-0.70032.4962-0.2858-0.19270.34630.12240.31310.1071-0.2788-0.2227-0.02280.42570.0441-0.03380.28410.02890.4788-32.9385-28.398628.4276
110.99780.2370.16462.16360.06421.3263-0.04660.04770.1934-0.10720.2504-0.0302-0.0947-0.0908-0.17280.3516-0.0375-0.03570.42860.06360.4103-17.4814-44.430814.7121
122.3566-1.26461.53282.01520.76492.2538-0.313-0.21030.69890.40960.3336-0.3183-0.14580.04510.05840.46760.0288-0.09630.3961-0.11170.5467-17.5721-30.671435.2095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 3:106
2X-RAY DIFFRACTION2chain A and resid 107:261
3X-RAY DIFFRACTION3chain A and resid 262:360
4X-RAY DIFFRACTION4chain B and resid 3:103
5X-RAY DIFFRACTION5chain B and resid 104:261
6X-RAY DIFFRACTION6chain B and resid 262:360
7X-RAY DIFFRACTION7chain C and resid 3:103
8X-RAY DIFFRACTION8chain C and resid 104:261
9X-RAY DIFFRACTION9chain C and resid 262:360
10X-RAY DIFFRACTION10chain D and resid 3:103
11X-RAY DIFFRACTION11chain D and resid 104:261
12X-RAY DIFFRACTION12chain D and resid 262:360

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