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- PDB-5hn3: Crystal structure of beta-decarboxylating dehydrogenase (TK0280) ... -

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Basic information

Entry
Database: PDB / ID: 5hn3
TitleCrystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis (apo form)
ComponentsHomoisocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / homoisocitrate dehydrogenase beta-decarboxylating dehydrogenase
Function / homology
Function and homology information


isocitrate dehydrogenase (NAD+) activity / 3-isopropylmalate dehydrogenase activity / isocitrate metabolic process / L-leucine biosynthetic process / NAD binding / magnesium ion binding
Similarity search - Function
Isopropylmalate/isohomocitrate 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
IMIDAZOLE / Homoisocitrate dehydrogenase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShimizu, T. / Tomita, T. / Nishiyama, M.
CitationJournal: Biochem. J. / Year: 2017
Title: Structure and function of an ancestral-type beta-decarboxylating dehydrogenase from Thermococcus kodakarensis
Authors: Shimizu, T. / Yin, L. / Yoshida, A. / Yokooji, Y. / Hachisuka, S.I. / Sato, T. / Tomita, T. / Nishida, H. / Atomi, H. / Kuzuyama, T. / Nishiyama, M.
History
DepositionJan 18, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homoisocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7994
Polymers38,6381
Non-polymers1613
Water3,963220
1
A: Homoisocitrate dehydrogenase
hetero molecules

A: Homoisocitrate dehydrogenase
hetero molecules

A: Homoisocitrate dehydrogenase
hetero molecules

A: Homoisocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,19616
Polymers154,5524
Non-polymers64512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area10500 Å2
ΔGint-75 kcal/mol
Surface area53860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.102, 91.447, 175.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Homoisocitrate dehydrogenase


Mass: 38637.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0280 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codonplus (RIL) / References: UniProt: Q5JFV8
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium chloride, imidazole / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→88 Å / Num. obs: 52021 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 31.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X0L

1x0l


Resolution: 1.7→88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.16 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23848 2647 5.1 %RANDOM
Rwork0.19992 ---
obs0.20187 49108 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.628 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 11 220 2775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192595
X-RAY DIFFRACTIONr_bond_other_d0.0010.022542
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9773509
X-RAY DIFFRACTIONr_angle_other_deg0.87635808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.535331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31922.605119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13815431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2361530
X-RAY DIFFRACTIONr_chiral_restr0.1020.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022962
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02600
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1772.9371327
X-RAY DIFFRACTIONr_mcbond_other2.1772.9351326
X-RAY DIFFRACTIONr_mcangle_it3.1374.3991657
X-RAY DIFFRACTIONr_mcangle_other3.1374.4021658
X-RAY DIFFRACTIONr_scbond_it2.5983.3451268
X-RAY DIFFRACTIONr_scbond_other2.5973.3461269
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0494.8691853
X-RAY DIFFRACTIONr_long_range_B_refined5.85524.0363028
X-RAY DIFFRACTIONr_long_range_B_other5.85424.0423029
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.699→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 183 -
Rwork0.284 3594 -
obs--99.39 %

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