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- PDB-3vl7: 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 a... -

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Basic information

Entry
Database: PDB / ID: 3vl7
Title3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 650 MPa
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNagae, T. / Watanabe, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase
Authors: Nagae, T. / Kawamura, T. / Chavas, L.M.G. / Niwa, K. / Hasegawa, M. / Kato, C. / Watanabe, N.
History
DepositionNov 29, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Jan 13, 2016Group: Structure summary
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 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)40,9414
Polymers40,6891
Non-polymers2523
Water3,171176
1
A: 3-isopropylmalate dehydrogenase
hetero molecules

A: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8828
Polymers81,3792
Non-polymers5036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area6680 Å2
ΔGint-66 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.135, 57.561, 75.067
Angle α, β, γ (deg.)90.00, 118.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-544-

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 (bacteria) / Strain: MR-1 / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.48 Å3/Da / Density % sol: 50.46 % / Mosaicity: 0.344 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, calcium chloride, HEPES, 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: 0.7 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17498 / % possible obs: 88.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.099 / Χ2: 2.602 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.242.70.3548822.486191.9
2.24-2.282.60.3378902.591190
2.28-2.322.70.3138684.296191.7
2.32-2.372.70.2799143.566190.9
2.37-2.422.60.2628805.476191.7
2.42-2.482.70.2449032.158191.1
2.48-2.542.70.2188822.348190.7
2.54-2.612.70.198883.363190.3
2.61-2.692.70.1628922.118190.7
2.69-2.772.70.1398771.65189.9
2.77-2.872.70.1248831.895190.6
2.87-2.992.70.1018852.054190.2
2.99-3.122.80.0858811.856189.6
3.12-3.292.70.0768722.041188.7
3.29-3.492.80.0618772.454188.3
3.49-3.762.70.0568541.952186.3
3.76-4.142.80.0518562.259186.8
4.14-4.742.80.0468522.281185.7
4.74-5.972.80.0558472.325184.4
5.97-502.90.0578153.064178.7

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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 3VKZ

3vkz


Resolution: 2.2→48.57 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.387 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 903 5.2 %RANDOM
Rwork0.1656 ---
obs0.1698 17434 88.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.93 Å2 / Biso mean: 17.0993 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20.45 Å2
2--0.12 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 14 176 2949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222874
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.9823892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57323.906128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47515503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4041524
X-RAY DIFFRACTIONr_chiral_restr0.1310.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212196
X-RAY DIFFRACTIONr_mcbond_it0.9671.51828
X-RAY DIFFRACTIONr_mcangle_it1.8622922
X-RAY DIFFRACTIONr_scbond_it3.10131046
X-RAY DIFFRACTIONr_scangle_it4.9534.5961
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 66 -
Rwork0.206 1131 -
all-1197 -
obs--83.3 %

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