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- PDB-1vlc: Crystal structure of 3-isopropylmalate dehydrogenase (TM0556) fro... -

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Basic information

Entry
Database: PDB / ID: 1vlc
TitleCrystal structure of 3-isopropylmalate dehydrogenase (TM0556) from Thermotoga maritima at 1.90 A resolution
Components3-isopropylmalate dehydrogenase
KeywordsDEHYDROGENASE / TM0556 / 3-ISOPROPYLMALATE DEHYDROGENASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / branched-chain amino acid biosynthetic process / L-leucine biosynthetic process / NAD binding / magnesium ion binding / 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
3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of 3-isopropylmalate dehydrogenase (TM0556) from Thermotoga maritima at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7382
Polymers40,7031
Non-polymers351
Water1,910106
1
A: 3-isopropylmalate dehydrogenase
hetero molecules

A: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4774
Polymers81,4062
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+11
Buried area4430 Å2
ΔGint-57 kcal/mol
Surface area27590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.780, 118.780, 56.699
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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


Mass: 40702.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: leuB, TM0556 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZ26, 3-isopropylmalate dehydrogenase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8456.62
22.9157.34
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop925.0% PEG-4000, 0.2M Li2SO4, 0.1M TRIS pH 9.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop7.520.0% PEG-8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL11-110.979454
SYNCHROTRONSSRL BL11-120.979251, 0.979508, 0.885567
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2004 / Details: flat mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(311) bent monochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794541
20.9792511
30.9795081
40.8855671
ReflectionResolution: 1.9→41.01 Å / Num. obs: 36394 / % possible obs: 99.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 39.46 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.6
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2598 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SHELXmodel building
autoSHARPphasing
SOLOMONphasing
REFMAC5.2.0003refinement
CCP4(SCALA)data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→41.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.093 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE DENSITY FOR LOOP 78-83,330-335 ARE POOR, MODEL FOR THESE TWO LOOPS ARE LESS RELIABLE 3. BIOLOGICAL UNIT AS A DIMER IS INFERRED ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE DENSITY FOR LOOP 78-83,330-335 ARE POOR, MODEL FOR THESE TWO LOOPS ARE LESS RELIABLE 3. BIOLOGICAL UNIT AS A DIMER IS INFERRED FROM HOMOLOGOUS PROTEINS (1A05,1CM7)
RfactorNum. reflection% reflectionSelection details
Rfree0.21822 1801 5 %RANDOM
Rwork0.18779 ---
obs0.18934 34079 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.46 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20.73 Å20 Å2
2--1.45 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 1 106 2830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222785
X-RAY DIFFRACTIONr_bond_other_d0.0020.022647
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9593775
X-RAY DIFFRACTIONr_angle_other_deg0.87236101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1975361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29723.333105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77915472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2431518
X-RAY DIFFRACTIONr_chiral_restr0.1090.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02543
X-RAY DIFFRACTIONr_nbd_refined0.2110.2556
X-RAY DIFFRACTIONr_nbd_other0.1780.22660
X-RAY DIFFRACTIONr_nbtor_other0.0870.21671
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.23
X-RAY DIFFRACTIONr_mcbond_it2.90231845
X-RAY DIFFRACTIONr_mcbond_other0.7483736
X-RAY DIFFRACTIONr_mcangle_it3.79552882
X-RAY DIFFRACTIONr_scbond_it6.49581061
X-RAY DIFFRACTIONr_scangle_it8.90811893
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21392
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 125 5.36 %
Rwork0.229 2207 -
obs--87.67 %
Refinement TLS params.Method: refined / Origin x: 18.1169 Å / Origin y: 86.0493 Å / Origin z: 21.2791 Å
111213212223313233
T-0.0666 Å2-0.0005 Å20.0279 Å2--0.0592 Å20.0235 Å2--0.0526 Å2
L0.3492 °2-0.3432 °2-0.0573 °2-2.2755 °20.4393 °2--0.3667 °2
S-0.0144 Å °-0.0637 Å °0.0768 Å °-0.0791 Å °0.0112 Å °-0.3824 Å °0.0599 Å °0.0158 Å °0.0032 Å °
Refinement TLS groupSelection: ALL

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