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- PDB-3wzx: S266A mutant 3-isopropylmalate dehydrogenase from Shewanella onei... -

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Basic information

Entry
Database: PDB / ID: 3wzx
TitleS266A mutant 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 0.1MPa - complex with IPM and Mg
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE / 3-ISOPROPYLMALATE DEHYDROGENASE / IPMDH / HIGH-PRESSURE / DIAMOND-ANVIL CELL / DAC
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / 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-ISOPROPYLMALIC ACID / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsNagae, T. / Watanabe, N.
CitationJournal: To be Published
Title: Pressure Adaptation of 3-Isopropylmalate Dehydrogenase from the Extremely Piezophilic Bacterium Shewanella benthica is Attributed to just One Amino Acid Substitution
Authors: Hamajima, Y. / Nagae, T. / Watanabe, N. / Kato-Yamada, Y. / Imai, T. / Kato, C.
History
DepositionOct 8, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
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.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.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.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)40,8743
Polymers40,6731
Non-polymers2002
Water3,693205
1
A: 3-isopropylmalate dehydrogenase
hetero molecules

A: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7486
Polymers81,3472
Non-polymers4014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area6570 Å2
ΔGint-37 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.299, 58.832, 76.663
Angle α, β, γ (deg.)90.000, 118.960, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21A-516-

HOH

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Components

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


Mass: 40673.305 Da / Num. of mol.: 1 / Mutation: S266A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: leuB, SO_4235 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codonplus(DE3) RIL
References: UniProt: Q8E9N3, 3-isopropylmalate dehydrogenase
#2: Chemical ChemComp-IPM / 3-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.38 % / Mosaicity: 0.318 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, NaCl, Na-HEPES, IPM, MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 34402 / Num. obs: 32337 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.05 / Χ2: 2.282 / Net I/σ(I): 20.3
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.86-1.892.20.35416033.07494.1
1.89-1.932.20.30616153.17494.2
1.93-1.962.20.23916242.66294.7
1.96-22.20.21116162.73895.1
2-2.052.20.19216012.48995.3
2.05-2.092.20.16816442.35295.6
2.09-2.152.20.14616632.17895.9
2.15-2.212.20.11816182.2695.6
2.21-2.272.20.10116461.99895.5
2.27-2.342.20.09516292.12895.9
2.34-2.432.20.08316612.21695.8
2.43-2.522.20.07716062.16995.3
2.52-2.642.20.06916581.89795.6
2.64-2.782.20.06216192.07794.7
2.78-2.952.30.05216502.06494.8
2.95-3.182.30.04216212.07794.3
3.18-3.52.30.03716201.97892.9
3.5-4.012.40.0315861.97591.6
4.01-5.052.40.0315672.01390.1
5.05-502.40.03214902.33883.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SERGUI(unified graphical user interface)data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VMJ

3vmj


Resolution: 1.9→22 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1683 / WRfactor Rwork: 0.1334 / FOM work R set: 0.8909 / SU B: 2.476 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1124 / SU Rfree: 0.1081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1694 1549 5.1 %RANDOM
Rwork0.1345 ---
obs0.1363 32337 93.68 %-
all-34402 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.86 Å2 / Biso mean: 27.23 Å2 / Biso min: 13.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20.11 Å2
2--0.52 Å2-0 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.9→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 13 205 2976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192825
X-RAY DIFFRACTIONr_bond_other_d0.0010.022738
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.9813813
X-RAY DIFFRACTIONr_angle_other_deg0.93836304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9325365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00423.659123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74115488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9671524
X-RAY DIFFRACTIONr_chiral_restr0.1260.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
X-RAY DIFFRACTIONr_mcbond_it2.6072.3631457
X-RAY DIFFRACTIONr_mcbond_other2.6072.3621456
X-RAY DIFFRACTIONr_mcangle_it3.7893.5271820
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 108 -
Rwork0.194 2089 -
all-2197 -
obs--93.61 %

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