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- PDB-3wzv: 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 a... -

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Basic information

Entry
Database: PDB / ID: 3wzv
Title3-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 7, 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.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)40,8903
Polymers40,6891
Non-polymers2002
Water3,333185
1
A: 3-isopropylmalate dehydrogenase
hetero molecules

A: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7806
Polymers81,3792
Non-polymers4014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area6560 Å2
ΔGint-36 kcal/mol
Surface area26770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.630, 58.867, 76.876
Angle α, β, γ (deg.)90.000, 118.920, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

21A-515-

HOH

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Components

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


Mass: 40689.305 Da / Num. of mol.: 1
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.: 185 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.7 % / Mosaicity: 0.39 °
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: Mar 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 32439 / Num. obs: 32231 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 / Χ2: 2.404 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.933.80.33416131.48699.4
1.93-1.973.70.30216021.59899.6
1.97-2.013.80.27115891.65199.7
2.01-2.053.80.2315851.70199.7
2.05-2.093.80.20816101.80199.9
2.09-2.143.80.17716331.91699.9
2.14-2.193.80.15516261.99199.9
2.19-2.253.80.13915852.14399.9
2.25-2.323.90.12616302.17199.9
2.32-2.393.80.1116132.311100
2.39-2.483.90.10716072.18699.9
2.48-2.583.90.09816162.35299.8
2.58-2.73.90.09116192.38599.6
2.7-2.843.90.0816112.56999.9
2.84-3.023.90.07116242.80399.4
3.02-3.253.90.0616162.91799.3
3.25-3.583.90.05216063.28499.3
3.58-4.093.90.04616223.60298.8
4.09-5.1640.0416013.60597.6
5.16-503.80.03816233.39795.6

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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→22.07 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1699 / WRfactor Rwork: 0.1331 / FOM work R set: 0.8897 / SU B: 2.418 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1052 / SU Rfree: 0.1042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1726 1632 5.1 %RANDOM
Rwork0.1363 ---
obs0.1382 32231 99.28 %-
all-32439 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.81 Å2 / Biso mean: 28.163 Å2 / Biso min: 13.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20.19 Å2
2--0.46 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.9→22.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 13 185 2957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192829
X-RAY DIFFRACTIONr_bond_other_d0.0010.022738
X-RAY DIFFRACTIONr_angle_refined_deg1.9491.9813814
X-RAY DIFFRACTIONr_angle_other_deg0.92936304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70723.659123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95315489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9351524
X-RAY DIFFRACTIONr_chiral_restr0.1280.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
X-RAY DIFFRACTIONr_mcbond_it2.9632.4561457
X-RAY DIFFRACTIONr_mcbond_other2.9632.4561456
X-RAY DIFFRACTIONr_mcangle_it4.3463.6661820
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.191 117 -
Rwork0.178 2222 -
all-2339 -
obs--98.78 %

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