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- PDB-2ztj: Crystal structure of homocitrate synthase from Thermus thermophil... -

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Basic information

Entry
Database: PDB / ID: 2ztj
TitleCrystal structure of homocitrate synthase from Thermus thermophilus complexed with alpha-ketoglutarate
ComponentsHomocitrate synthase
KeywordsTRANSFERASE / (beta/alpha)8 TIM barrel / substrate complex / Amino-acid biosynthesis / Lysine biosynthesis
Function / homology
Function and homology information


homocitrate synthase / homocitrate synthase activity / citrate synthase activity / lysine biosynthetic process via aminoadipic acid / metal ion binding / cytoplasm
Similarity search - Function
H-NS DNA Binding Protein - #20 / H-NS DNA Binding Protein / : / Homocitrate synthase, fungi/archaea / Alpha-isopropylmalate and homocitrate synthases signature 2. / Alpha-isopropylmalate and homocitrate synthases signature 1. / Alpha-isopropylmalate/homocitrate synthase, conserved site / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. ...H-NS DNA Binding Protein - #20 / H-NS DNA Binding Protein / : / Homocitrate synthase, fungi/archaea / Alpha-isopropylmalate and homocitrate synthases signature 2. / Alpha-isopropylmalate and homocitrate synthases signature 1. / Alpha-isopropylmalate/homocitrate synthase, conserved site / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Few Secondary Structures / Irregular / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / COPPER (II) ION / Homocitrate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsOkada, T. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus
Authors: Okada, T. / Tomita, T. / Wulandari, A.P. / Kuzuyama, T. / Nishiyama, M.
History
DepositionOct 6, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 25, 2012Group: Advisory / Database references / Experimental preparation
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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

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Assembly

Deposited unit
A: Homocitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2843
Polymers43,0741
Non-polymers2102
Water7,548419
1
A: Homocitrate synthase
hetero molecules

A: Homocitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5676
Polymers86,1482
Non-polymers4194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area6020 Å2
ΔGint-32 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.645, 135.645, 127.102
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

21A-562-

HOH

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Components

#1: Protein Homocitrate synthase


Mass: 43074.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: hcs / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL-CodonPlus (DE3) / References: UniProt: O87198, homocitrate synthase
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 1 IN THE DATABASE HOSC_THET2, AC O87198. A104PRO IS CONFLICT OF HOSC_THET2.

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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: 3.92 Å3/Da / Density % sol: 68.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.0M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONPhoton Factory BL-5A20.97945, 0.97934, 0.96421
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDNov 7, 2007mirrors
ADSC QUANTUM 3152CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SiSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979451
30.979341
40.964211
ReflectionResolution: 1.8→50 Å / Num. all: 64069 / Num. obs: 64069 / Observed criterion σ(I): 3.9 / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.1
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→30.66 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.702 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22391 3238 5.1 %RANDOM
Rwork0.19908 ---
obs0.20034 60741 99.95 %-
all-60741 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.578 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 11 419 2878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONc_angle_deg0.0130.0222501
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9693387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2625310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18423.448116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19715428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1351522
X-RAY DIFFRACTIONr_chiral_restr0.1070.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021899
X-RAY DIFFRACTIONr_nbd_refined0.2250.21459
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21745
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2339
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.245
X-RAY DIFFRACTIONr_mcbond_it0.8311.51602
X-RAY DIFFRACTIONr_mcangle_it1.26822505
X-RAY DIFFRACTIONr_scbond_it2.25431011
X-RAY DIFFRACTIONr_scangle_it3.5174.5882
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 260 -
Rwork0.267 4348 -
obs--99.72 %

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