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- PDB-4yb4: Crystal structure of homoisocitrate dehydrogenase from Thermus th... -

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Basic information

Entry
Database: PDB / ID: 4yb4
TitleCrystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium ion (II) and NADH
ComponentsHomoisocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / Homoisocitrate dehydrogenase Thermus thermophilus
Function / homology
Function and homology information


isocitrate-homoisocitrate dehydrogenase / homoisocitrate dehydrogenase activity / isocitrate dehydrogenase (NAD+) activity / lysine biosynthetic process via aminoadipic acid / isocitrate metabolic process / tricarboxylic acid cycle / metal ion binding
Similarity search - Function
Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Isocitrate/homoisocitrate dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTakahashi, K. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
CitationJournal: To Be Published
Title: Structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium(II) and NADH
Authors: Takahashi, K. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
History
DepositionFeb 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 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_asym_id / _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_asym_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_asym_id / _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_asym_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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homoisocitrate dehydrogenase
B: Homoisocitrate dehydrogenase
C: Homoisocitrate dehydrogenase
D: Homoisocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,54570
Polymers143,8694
Non-polymers8,67666
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16080 Å2
ΔGint-113 kcal/mol
Surface area45730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.663, 159.663, 148.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Homoisocitrate dehydrogenase / HICDH


Mass: 35967.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / Gene: hicd, hdh, hicdh, TT_C1012 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q72IW9, homoisocitrate dehydrogenase

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Non-polymers , 6 types, 629 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-48Y / (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid


Mass: 206.150 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H10O7
#4: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5), 1.5 M Ammonium sulfate, 12 % (v/v) Glycerol

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 66916 / % possible obs: 95.1 % / Observed criterion σ(F): 3.9 / Observed criterion σ(I): 3.9 / Redundancy: 3.9 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 18.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Coot0.8-prerefinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X0L

1x0l


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.489 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED GN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20495 2997 4.7 %RANDOM
Rwork0.14995 ---
obs0.15255 60576 95.09 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.805 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10076 0 530 563 11169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910724
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210456
X-RAY DIFFRACTIONr_angle_refined_deg1.4572.03514564
X-RAY DIFFRACTIONr_angle_other_deg0.93.00724028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77451328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.27222.952420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.534151728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.13315104
X-RAY DIFFRACTIONr_chiral_restr0.0810.21742
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111688
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022200
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_it1.5373.0185324
X-RAY DIFFRACTIONr_mcbond_other1.5343.0175323
X-RAY DIFFRACTIONr_mcangle_it2.464.5196648
X-RAY DIFFRACTIONr_mcangle_other2.4614.526649
X-RAY DIFFRACTIONr_scbond_it2.4933.545400
X-RAY DIFFRACTIONr_scbond_other2.4933.545400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0045.157917
X-RAY DIFFRACTIONr_long_range_B_refined6.51224.61512085
X-RAY DIFFRACTIONr_long_range_B_other6.51224.61812086
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 240 -
Rwork0.196 --
obs--96.34 %

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