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- PDB-3ty4: Crystal structure of homoisocitrate dehydrogenase from Schizosacc... -

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Basic information

Entry
Database: PDB / ID: 3ty4
TitleCrystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe
ComponentsProbable homoisocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / B-hydroxyacid oxidative decarboxylase / amino-acid biosynthesis / lysine biosynthesis
Function / homology
Function and homology information


homoisocitrate dehydrogenase / homoisocitrate dehydrogenase activity / lysine biosynthetic process / isocitrate dehydrogenase (NAD+) activity / lysine biosynthetic process via aminoadipic acid / isocitrate metabolic process / tricarboxylic acid cycle / NAD binding / magnesium ion binding / mitochondrion / cytoplasm
Similarity search - Function
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
Homoisocitrate dehydrogenase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsBulfer, S.L. / Hendershot, J.M. / Trievel, R.C.
CitationJournal: Proteins / Year: 2012
Title: Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe.
Authors: Bulfer, S.L. / Hendershot, J.M. / Trievel, R.C.
History
DepositionSep 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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 / 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 / _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: Probable homoisocitrate dehydrogenase
B: Probable homoisocitrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,20612
Polymers79,2852
Non-polymers92110
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-30 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.851, 94.452, 76.076
Angle α, β, γ (deg.)90.000, 106.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable homoisocitrate dehydrogenase


Mass: 39642.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: ATCC 38366 / 972 / Gene: lys12, SPAC31G5.04 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: O14104, homoisocitrate dehydrogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3550, Li acetate, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 25, 2010
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→25 Å / Num. all: 103345 / Num. obs: 103345 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.055 / Χ2: 1.042 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.614.30.45997871.031194.2
1.61-1.675.60.396102241.035199
1.67-1.756.80.322103551.0771100
1.75-1.847.30.232103961.0891100
1.84-1.957.40.159104031.0561100
1.95-2.17.50.109103991.0311100
2.1-2.317.50.088104210.9721100
2.31-2.657.60.064104001.091100
2.65-3.347.50.046104381.0661100
3.34-257.30.035105220.97199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3TY3

3ty3


Resolution: 1.55→24.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.2155 / WRfactor Rwork: 0.1879 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.8649 / SU B: 3.322 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0856 / SU Rfree: 0.0851 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 5157 5 %RANDOM
Rwork0.1879 ---
all0.1893 102756 --
obs0.1893 102756 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.67 Å2 / Biso mean: 22.1474 Å2 / Biso min: 3.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.31 Å2
2--0.3 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.55→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5309 0 60 500 5869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225705
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9837787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2965788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07623.901223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95515960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6171541
X-RAY DIFFRACTIONr_chiral_restr0.0930.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214291
X-RAY DIFFRACTIONr_mcbond_it0.741.53695
X-RAY DIFFRACTIONr_mcangle_it1.24925987
X-RAY DIFFRACTIONr_scbond_it2.07532010
X-RAY DIFFRACTIONr_scangle_it3.3194.51769
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 352 -
Rwork0.281 6731 -
all-7083 -
obs--93.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8586-0.0250.49540.61080.02321.1572-0.03180.0820.0444-0.00410.0233-0.0307-0.05780.02920.00850.0213-0.01740.01560.033-0.01330.01950.7074.569.763
20.51050.1320.24330.66570.00571.68390.0076-0.0806-0.02110.0424-0.0252-0.01030.12450.02580.01760.02180.01510.00720.0449-0.00470.0221-0.14-3.69443.438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 360
2X-RAY DIFFRACTION2B4 - 360

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