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

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Basic information

Entry
Database: PDB / ID: 2ztk
TitleCrystal structure of homocitrate synthase from Thermus thermophilus complexed with homocitrate
ComponentsHomocitrate synthase
KeywordsTRANSFERASE / (beta/alpha)8 TIM barrel / product 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
COPPER (II) ION / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Homocitrate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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: Advisory / Version format compliance
Revision 1.2Jan 25, 2012Group: Database references
Revision 1.3Nov 1, 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_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)43,3443
Polymers43,0741
Non-polymers2702
Water6,684371
1
A: Homocitrate synthase
hetero molecules

A: Homocitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6886
Polymers86,1482
Non-polymers5394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area6260 Å2
ΔGint-37 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.508, 135.508, 127.062
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-478-

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-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10O7
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


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


Mass: 18.015 Da / Num. of mol.: 371 / 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: 3.91 Å3/Da / Density % sol: 68.53 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2007
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.96→50 Å / Num. all: 48641 / Num. obs: 48641 / % possible obs: 99.6 % / Observed criterion σ(I): 3.5 / Rmerge(I) obs: 0.073 / Net I/σ(I): 53.7
Reflection shellResolution: 1.96→2.03 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZTJ

2ztj


Resolution: 1.96→44.36 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.782 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22177 2504 5.1 %RANDOM
Rwork0.19296 ---
obs0.19442 46920 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.044 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.96→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 15 371 2834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222505
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9723394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.9675310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49123.448116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03215428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.111522
X-RAY DIFFRACTIONr_chiral_restr0.1520.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211899
X-RAY DIFFRACTIONr_mcbond_it0.6971.51550
X-RAY DIFFRACTIONr_mcangle_it1.30622505
X-RAY DIFFRACTIONr_scbond_it2.2323955
X-RAY DIFFRACTIONr_scangle_it3.9084.5889
LS refinement shellResolution: 1.964→2.015 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 171 -
Rwork0.272 3361 -
obs--98.27 %
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)
11.06340.2010.12521.12050.04060.92830.0119-0.0485-0.21660.0854-0.0008-0.10530.18640.0309-0.01110.13410.00820.00630.15120.00290.1283-37.406739.9042-10.9729
20.68110.0819-0.05891.2786-0.15530.7357-0.0045-0.0371-0.06710.02990.00130.07080.055-0.05850.00330.07590.0036-0.00670.0944-0.00420.0752-49.479742.5642-21.3381
30.92640.3128-0.27481.1777-0.31982.2125-0.04790.20590.366-0.08560.03510.1507-0.3951-0.26080.01280.1963-0.0180.0020.176-0.02270.2024-43.938567.5291-25.6818
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 142
2X-RAY DIFFRACTION2A143 - 249
3X-RAY DIFFRACTION3A250 - 320

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