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- PDB-3vmk: 3-isopropylmalate dehydrogenase from Shewanella benthica DB21 MT-2 -

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Basic information

Entry
Database: PDB / ID: 3vmk
Title3-isopropylmalate dehydrogenase from Shewanella benthica DB21 MT-2
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE / DECARBOXYLATING DEHYDROGENASE
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / cytoplasm
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-ISOPROPYLMALIC ACID / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesShewanella benthica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsNagae, T. / Watanabe, N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structural analysis of 3-isopropylmalate dehydrogenase from the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1
Authors: Nagae, T. / Kato, C. / Watanabe, N.
History
DepositionDec 13, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_asym_id / _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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8308
Polymers81,3582
Non-polymers4726
Water12,773709
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-60 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.972, 59.208, 119.779
Angle α, β, γ (deg.)90.00, 95.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-isopropylmalate dehydrogenase /


Mass: 40679.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella benthica (bacteria) / Strain: DB21 MT-2 / Gene: leuB / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Codonplus(de3) Ril
References: UniProt: D2YZL2, 3-isopropylmalate dehydrogenase
#2: Chemical ChemComp-IPM / 3-ISOPROPYLMALIC ACID / Isopropylmalic acid


Mass: 176.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12O5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.26 Å3/Da / Density % sol: 45.48 % / Mosaicity: 0.517 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: PEG 3350, sodium chloride, HEPES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 118167 / % possible obs: 98.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Χ2: 1.647 / Net I/σ(I): 19.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.48-1.513.20.32257101.629196.1
1.51-1.533.40.27158641.632197.5
1.53-1.563.70.23458151.674198
1.56-1.593.70.20358981.66198.1
1.59-1.633.70.16859071.652198.3
1.63-1.673.70.15359041.646198.6
1.67-1.713.70.13559221.609198.7
1.71-1.753.70.11359341.595198.9
1.75-1.813.70.09759491.628199.1
1.81-1.863.70.08159881.615199.2
1.86-1.933.70.06359571.611199.4
1.93-2.013.80.05459521.618199.4
2.01-2.13.80.04559891.546199.6
2.1-2.213.80.03860051.567199.7
2.21-2.353.80.03360251.518199.8
2.35-2.533.80.0360471.52199.9
2.53-2.793.70.02860221.579199.9
2.79-3.193.70.02560411.564199.8
3.19-4.023.50.02658781.68196.3
4.02-503.20.03553602.713186.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SERGUI(unified graphical user interface)data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VKZ

3vkz


Resolution: 1.48→25.77 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.418 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 5928 5 %RANDOM
Rwork0.1934 ---
obs0.1953 118063 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.42 Å2 / Biso mean: 19.8483 Å2 / Biso min: 6.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å2-0.36 Å2
2--1.01 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.48→25.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5594 0 28 709 6331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0225798
X-RAY DIFFRACTIONr_angle_refined_deg2.4461.9797854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13724.291254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01115999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.011538
X-RAY DIFFRACTIONr_chiral_restr0.1770.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214430
X-RAY DIFFRACTIONr_mcbond_it1.5341.53696
X-RAY DIFFRACTIONr_mcangle_it2.26125900
X-RAY DIFFRACTIONr_scbond_it3.32632102
X-RAY DIFFRACTIONr_scangle_it5.0134.51939
LS refinement shellResolution: 1.481→1.519 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 426 -
Rwork0.26 8004 -
all-8430 -
obs--95.42 %

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