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- PDB-3vml: Chimera 3-isopropylmalate dehydrogenase between Shewanella oneide... -

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Basic information

Entry
Database: PDB / ID: 3vml
TitleChimera 3-isopropylmalate dehydrogenase between Shewanella oneidensis MR-1 (O) and Shewanella benthica DB21 MT-2 (M) from N-terminal: 20% O middle 70% M residual 10% O
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 / cytosol / 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 / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
Shewanella benthica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsNagae, T. / Watanabe, N.
CitationJournal: To be Published
Title: Structure analysis of chimeric 3-isopropylmalate dehydrogenase between the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1
Authors: Hamajima, Y. / Nagae, T. / Watanabe, N. / Kato, C.
History
DepositionDec 13, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
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_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_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_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_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

Downloads & links

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Assembly

Deposited unit
A: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9614
Polymers40,7251
Non-polymers2363
Water8,503472
1
A: 3-isopropylmalate dehydrogenase
hetero molecules

A: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9238
Polymers81,4512
Non-polymers4726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6400 Å2
ΔGint-62 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.008, 107.523, 83.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-519-

HOH

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Components

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


Mass: 40725.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera protein of 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 (UNP Q8E9N3 residues 2-68), 3-isopropylmalate dehydrogenase from Shewanella benthica DB21 MT-2 (UNP D2YZL2 ...Details: chimera protein of 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 (UNP Q8E9N3 residues 2-68), 3-isopropylmalate dehydrogenase from Shewanella benthica DB21 MT-2 (UNP D2YZL2 residues 69-328), and 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 (UNP Q8E9N3 residues 329-364)
Source: (gene. exp.) Shewanella oneidensis (bacteria), (gene. exp.) Shewanella benthica (bacteria)
Strain: MR-1, DB21 MT-2, MR-1 / Gene: leuB, SO_4235 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Codonplus(de3) Ril
References: UniProt: Q8E9N3, UniProt: D2YZL2, 3-isopropylmalate dehydrogenase
#2: Chemical ChemComp-IPM / 3-ISOPROPYLMALIC ACID / Isopropylmalic acid


Mass: 176.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12O5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 7.5
Details: PEG 3350, sodium chloride, HEPES, pH 7.5, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 56022 / % possible obs: 98.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.56-1.593.50.403194.1
1.59-1.624.10.352198.6
1.62-1.654.40.32199.9
1.65-1.684.50.295199.8
1.68-1.724.50.27199.9
1.72-1.764.50.227199.8
1.76-1.84.50.197199.6
1.8-1.854.50.17199.8
1.85-1.94.50.147199.5
1.9-1.974.50.114199.4
1.97-2.044.50.102199.3
2.04-2.124.60.087199.3
2.12-2.214.60.076199
2.21-2.334.50.067198.7
2.33-2.484.60.061198.7
2.48-2.674.60.057198.2
2.67-2.944.60.053197.8
2.94-3.364.60.047197
3.36-4.234.60.043196.5
4.23-504.40.043193.6

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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 1A05

1a05


Resolution: 1.56→33.25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.446 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20903 2830 5.1 %RANDOM
Rwork0.17749 ---
obs0.17907 53159 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.924 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2--0.34 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.56→33.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 14 472 3239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0222864
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3641.9843880
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0345381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4124.344122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22115506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4621519
X-RAY DIFFRACTIONr_chiral_restr0.1710.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212171
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_it1.5121.51826
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.30722921
X-RAY DIFFRACTIONr_scbond_it3.51831038
X-RAY DIFFRACTIONr_scangle_it5.3394.5949
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.601 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 194 -
Rwork0.255 3737 -
obs--94.54 %

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