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

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Basic information

Entry
Database: PDB / ID: 3wzw
Title3-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: 1.8 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)40,8903
Polymers40,6891
Non-polymers2002
Water4,414245
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 area6450 Å2
ΔGint-34 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.690, 57.669, 75.467
Angle α, β, γ (deg.)90.000, 118.660, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-532-

HOH

21A-547-

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.: 245 / 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: 2.41 Å3/Da / Density % sol: 48.95 % / Mosaicity: 0.104 °
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: 1.8→50 Å / Num. all: 35836 / Num. obs: 33002 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.076 / Χ2: 2.436 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allRpim(I) allRrim(I) allΧ2% possible all
1.8-1.833.80.4916930.2790.5671.81994
1.83-1.863.80.43816310.2460.5051.83293.6
1.86-1.93.80.34916900.1950.4021.89393.9
1.9-1.943.70.30716480.1740.3551.92293.6
1.94-1.983.70.3416650.1940.3932.2493.3
1.98-2.033.10.29716190.1890.3553.63790.6
2.03-2.083.10.25815800.1630.3063.29989.5
2.08-2.133.70.19816500.1140.232.73392.7
2.13-2.23.70.13516740.0780.1572.20293.5
2.2-2.273.80.11716890.0670.1352.23693.8
2.27-2.353.80.10216460.0580.1182.22492.8
2.35-2.443.80.09216820.0520.1062.31192.7
2.44-2.553.80.08316380.0460.0952.41992.4
2.55-2.693.80.07316610.0410.0842.30292.6
2.69-2.863.80.06416380.0360.0742.48291.7
2.86-3.083.90.05716490.0320.0662.62192.1
3.08-3.393.90.05216330.0290.0592.81390.9
3.39-3.883.90.04816500.0260.0552.89491.2
3.88-4.883.90.04316450.0240.052.80290.2
4.88-503.80.04216210.0240.0492.59187

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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: 1.8→36.23 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.1704 / FOM work R set: 0.8263 / SU B: 2.759 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1296 / SU Rfree: 0.1297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 1649 5 %RANDOM
Rwork0.1734 ---
obs0.1758 33002 91.73 %-
all-35836 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.91 Å2 / Biso mean: 23.025 Å2 / Biso min: 10.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å20.16 Å2
2--0.58 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 13 245 3017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192826
X-RAY DIFFRACTIONr_bond_other_d0.0010.022737
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.9813814
X-RAY DIFFRACTIONr_angle_other_deg0.98236303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9655365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95923.659123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05715489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8221524
X-RAY DIFFRACTIONr_chiral_restr0.1370.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
X-RAY DIFFRACTIONr_mcbond_it2.2362.0091457
X-RAY DIFFRACTIONr_mcbond_other2.2362.0091456
X-RAY DIFFRACTIONr_mcangle_it3.343.0011820
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 113 -
Rwork0.231 2217 -
all-2330 -
obs--89.17 %

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