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- PDB-3ah3: Crystal structure of LR5-1, 3-isopropylmalate dehydrogenase creat... -

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Basic information

Entry
Database: PDB / ID: 3ah3
TitleCrystal structure of LR5-1, 3-isopropylmalate dehydrogenase created by directed evolution
ComponentsHomoisocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / 3-isopropylmalate dehydrogenase / homoisocitrate dehydrogenase / directed evolution
Function / homology
Function and homology information


isocitrate-homoisocitrate dehydrogenase / homoisocitrate dehydrogenase activity / isocitrate dehydrogenase (NAD+) activity / lysine biosynthetic process via aminoadipic acid / isocitrate metabolic process / tricarboxylic acid cycle / metal ion binding
Similarity search - Function
Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isocitrate/homoisocitrate dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTomita, T. / Suzuki, Y. / Kuzuyama, T. / Nishiyama, M.
CitationJournal: Biochem.J. / Year: 2010
Title: Enhancement of the latent 3-isopropylmalate dehydrogenase activity of promiscuous homoisocitrate dehydrogenase by directed evolution
Authors: Suzuki, Y. / Asada, K. / Miyazaki, J. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
History
DepositionApr 13, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...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 / 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: Homoisocitrate dehydrogenase
B: Homoisocitrate dehydrogenase
C: Homoisocitrate dehydrogenase
D: Homoisocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,51619
Polymers143,4494
Non-polymers1,06715
Water5,603311
1
A: Homoisocitrate dehydrogenase
C: Homoisocitrate dehydrogenase
hetero molecules

A: Homoisocitrate dehydrogenase
C: Homoisocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,57820
Polymers143,4494
Non-polymers1,12916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9040 Å2
ΔGint-70 kcal/mol
Surface area52520 Å2
MethodPISA
2
B: Homoisocitrate dehydrogenase
D: Homoisocitrate dehydrogenase
hetero molecules

B: Homoisocitrate dehydrogenase
D: Homoisocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,45418
Polymers143,4494
Non-polymers1,00514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9030 Å2
ΔGint-73 kcal/mol
Surface area53900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.335, 61.737, 170.054
Angle α, β, γ (deg.)90.00, 98.28, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Homoisocitrate dehydrogenase / LR5-1


Mass: 35862.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: LR5-1 / Plasmid: pET-LR5-1, pET 26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RILCodonPlus / References: UniProt: Q72IW9, homoisocitrate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE MUTATIONS HAVE BEEN INTRODUCED THROUGH RANDOM MUTATION/SCREENING PROCESS.

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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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 3350, 27% MPD, 100mM Imidazole (pH 6.5), 200mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 67714 / Num. obs: 67714 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 17
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.346

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X0L

1x0l


Resolution: 2.4→49.78 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.611 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26734 3406 5.1 %RANDOM
Rwork0.21594 ---
obs0.21849 63878 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.166 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.05 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10036 0 64 311 10411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210371
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.99514094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.21651360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80623.167420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.936151751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8415100
X-RAY DIFFRACTIONr_chiral_restr0.070.21664
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217764
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_it0.4071.56668
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.771210752
X-RAY DIFFRACTIONr_scbond_it1.06333703
X-RAY DIFFRACTIONr_scangle_it1.9024.53326
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.396→2.458 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 251 -
Rwork0.3 4429 -
obs--93.94 %
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)
10.15820.1223-0.25370.6949-0.22951.02370.0202-0.0136-0.0126-0.0196-0.0173-0.08970.0450.0766-0.00290.03560.0035-0.00320.0893-0.00350.101528.47213.166155.6095
21.036-0.13160.63320.80730.01750.6569-0.00910.06290.0151-0.2317-0.0082-0.0307-0.05170.08470.01730.16620.0020.00810.05330.0080.049716.9268-14.026922.8118
30.91120.48360.00691.29270.28741.4493-0.0002-0.03470.0792-0.0847-0.04270.3442-0.0474-0.49540.0430.01250.0217-0.00590.2210.01940.18386.2454-11.17668.9354
40.6354-0.32460.14541.46040.25272.0648-0.025-0.1494-0.03210.19640.00410.3502-0.0747-0.5570.02090.240.0376-0.00530.22180.01420.2017-9.188310.384726.5089
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 334
2X-RAY DIFFRACTION2B2 - 334
3X-RAY DIFFRACTION3C2 - 334
4X-RAY DIFFRACTION4D2 - 334

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