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- PDB-5hn5: Crystal structure of beta-decarboxylating dehydrogenase (TK0280) ... -

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Basic information

Entry
Database: PDB / ID: 5hn5
TitleCrystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and isocitrate
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 / tricarboxylic acid cycle / 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
ISOCITRIC ACID / : / Homoisocitrate dehydrogenase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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
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.ptnr2_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homoisocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0034
Polymers38,6381
Non-polymers3653
Water23413
1
A: Homoisocitrate dehydrogenase
hetero molecules

A: Homoisocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0068
Polymers77,2762
Non-polymers7306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area5980 Å2
ΔGint-55 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.372, 80.372, 141.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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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-ICT / ISOCITRIC ACID / Isocitric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Tris, sodium chloride, 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→141.06 Å / Num. obs: 15751 / % possible obs: 99.2 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 41.2
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 3.3 / % 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: 5HN4

5hn4


Resolution: 2.55→141.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.91 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25682 778 5 %RANDOM
Rwork0.19748 ---
obs0.20032 14808 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.118 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.55→141.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 22 13 2530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192562
X-RAY DIFFRACTIONr_bond_other_d0.0020.022513
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9823469
X-RAY DIFFRACTIONr_angle_other_deg0.8873.0015745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32722.672116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84315424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1521529
X-RAY DIFFRACTIONr_chiral_restr0.0880.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02579
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_it3.9176.3781312
X-RAY DIFFRACTIONr_mcbond_other3.9186.3741311
X-RAY DIFFRACTIONr_mcangle_it5.6649.5681640
X-RAY DIFFRACTIONr_mcangle_other5.6639.5721641
X-RAY DIFFRACTIONr_scbond_it4.5926.8511250
X-RAY DIFFRACTIONr_scbond_other4.596.8511251
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.93410.0741830
X-RAY DIFFRACTIONr_long_range_B_refined8.83950.5242854
X-RAY DIFFRACTIONr_long_range_B_other8.83750.532855
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.552→2.618 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 54 -
Rwork0.251 1076 -
obs--98.43 %

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