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

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Basic information

Entry
Database: PDB / ID: 3vkz
Title3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at atmospheric pressure
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 / MOLECULAR REPLACEMENT / Resolution: 1.84 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 28, 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
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
Water3,315184
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 area6830 Å2
ΔGint-67 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.797, 59.003, 76.754
Angle α, β, γ (deg.)90.00, 119.07, 90.00
Int Tables number5
Space group name H-MC121

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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.: 184 / 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: 2.63 Å3/Da / Density % sol: 53.3 % / Mosaicity: 0.458 °
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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 31951 / % possible obs: 89.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.066 / Χ2: 2.921 / Net I/σ(I): 21.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.84-1.873.80.40816122.543189.3
1.87-1.913.80.35215782.566189.3
1.91-1.943.80.28815752.517189.6
1.94-1.983.80.25715962.391190.2
1.98-2.033.70.22816172.605190.3
2.03-2.073.80.216202.525190.9
2.07-2.123.80.17315852.727190.8
2.12-2.183.80.14816222.493191
2.18-2.253.80.12916162.677191
2.25-2.323.80.11216292.733190.7
2.32-2.43.70.10316142.715191.3
2.4-2.53.80.09316502.885191.5
2.5-2.613.80.08416262.694191.3
2.61-2.753.80.07516122.74190.6
2.75-2.923.80.06216023.019190.1
2.92-3.153.80.05316082.927190.1
3.15-3.463.90.04715983.483189.1
3.46-3.963.90.04315893.421187.9
3.96-4.993.90.04615504.187185.4
4.99-503.90.04914524.679178.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A05

1a05


Resolution: 1.84→22.15 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.161 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 1620 5.1 %RANDOM
Rwork0.142 ---
obs0.1442 31907 89.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.72 Å2 / Biso mean: 26.2431 Å2 / Biso min: 9.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20.08 Å2
2--0.22 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.84→22.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 14 184 2957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222874
X-RAY DIFFRACTIONr_angle_refined_deg2.2071.9823892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9975381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86623.906128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55415503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0521524
X-RAY DIFFRACTIONr_chiral_restr0.1840.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212196
X-RAY DIFFRACTIONr_mcbond_it1.5811.51828
X-RAY DIFFRACTIONr_mcangle_it2.8122922
X-RAY DIFFRACTIONr_scbond_it4.30531046
X-RAY DIFFRACTIONr_scangle_it6.8714.5961
LS refinement shellResolution: 1.838→1.885 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 107 -
Rwork0.199 2140 -
all-2247 -
obs--86.39 %

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