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

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Basic information

Entry
Database: PDB / ID: 3wzy
TitleS266A mutant 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 580MPa - 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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
Water5,909328
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 area6410 Å2
ΔGint-35 kcal/mol
Surface area26050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.314, 57.417, 75.362
Angle α, β, γ (deg.)90.000, 118.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

21A-527-

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.: 328 / 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

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.41 % / Mosaicity: 0.171 °
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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.75 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 55786 / Num. obs: 50565 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.063 / Χ2: 2.177 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allRpim(I) allRrim(I) allΧ2% possible all
1.55-1.582.20.53525520.3720.6581.54592.5
1.58-1.612.50.52325820.3450.6341.87592.9
1.61-1.642.60.4826500.3050.5751.84593.7
1.64-1.672.60.4125600.2620.4921.81193.8
1.67-1.712.60.34125740.2180.4091.83293.9
1.71-1.752.60.3126220.1990.3722.03994
1.75-1.792.60.27626650.180.3332.07894.4
1.79-1.842.60.20625820.1340.2491.96193.7
1.84-1.892.60.16625960.1090.2012.05993.1
1.89-1.952.70.13725330.0890.1662.24291.9
1.95-2.022.60.13225380.0860.1592.94290.7
2.02-2.12.60.11224460.0750.1372.83787.9
2.1-2.22.70.07624850.050.0922.31190.1
2.2-2.322.70.06824840.0450.0822.26289.2
2.32-2.462.70.05725000.0370.0692.15989
2.46-2.652.80.0524720.0320.062.16788.6
2.65-2.922.80.04424850.0280.0532.27688.5
2.92-3.342.80.03924430.0250.0472.46787
3.34-4.212.90.03524230.0220.0422.42886
4.21-502.90.03323730.0220.042.22882.3

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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: 1.55→36.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2117 / WRfactor Rwork: 0.1755 / FOM work R set: 0.8059 / SU B: 1.84 / SU ML: 0.065 / SU R Cruickshank DPI: 0.0891 / SU Rfree: 0.0919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 2587 5.1 %RANDOM
Rwork0.1851 ---
obs0.187 50565 90.5 %-
all-55786 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.22 Å2 / Biso mean: 20.779 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20.19 Å2
2--0.43 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.55→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 13 328 3099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192825
X-RAY DIFFRACTIONr_bond_other_d0.0010.022738
X-RAY DIFFRACTIONr_angle_refined_deg2.2011.9813813
X-RAY DIFFRACTIONr_angle_other_deg0.98936304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0165365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26623.659123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99915488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7541524
X-RAY DIFFRACTIONr_chiral_restr0.150.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
X-RAY DIFFRACTIONr_mcbond_it2.1761.7751457
X-RAY DIFFRACTIONr_mcbond_other2.1741.7741456
X-RAY DIFFRACTIONr_mcangle_it3.2262.6611820
LS refinement shellResolution: 1.548→1.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 198 -
Rwork0.294 3535 -
all-3733 -
obs--90.54 %

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