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- PDB-3a9i: Crystal structure of homocitrate synthase from Thermus thermophil... -

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Basic information

Entry
Database: PDB / ID: 3a9i
TitleCrystal structure of homocitrate synthase from Thermus thermophilus complexed with Lys
ComponentsHomocitrate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / homocitrate synthase / Lysine complex / Amino-acid biosynthesis / Lysine biosynthesis / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
: / 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. / Aldolase class I / Aldolase-type TIM barrel ...: / 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. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / LYSINE / Homocitrate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 28, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Jan 25, 2012Group: Database references / Structure summary
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_conn_angle / struct_conn / struct_site
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.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_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: Homocitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4513
Polymers42,2451
Non-polymers2062
Water3,333185
1
A: Homocitrate synthase
hetero molecules

A: Homocitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9036
Polymers84,4902
Non-polymers4124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6900 Å2
ΔGint-25 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.281, 96.025, 77.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Homocitrate synthase /


Mass: 42245.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL-CodonPlus / References: UniProt: O87198, homocitrate synthase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1.7582 Å3/Da / Density % sol: 30.0437 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8M Ammonium sulfate, 0.1M MES (pH6.5), 0.01M Cobaltous chloride hexahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 210r / Detector: CCD / Date: Oct 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 28047 / Num. obs: 28047 / Redundancy: 7.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 35.098
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1378

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homocitrate synthase (PDB ID 2ZTJ)

2ztj


Resolution: 1.8→35.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.582 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21338 1402 5 %RANDOM
Rwork0.1706 ---
obs0.17285 26532 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.122 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 11 185 2940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222805
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9673800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4195344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7723.582134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31215483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4671524
X-RAY DIFFRACTIONr_chiral_restr0.0910.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212129
X-RAY DIFFRACTIONr_mcbond_it0.6781.51729
X-RAY DIFFRACTIONr_mcangle_it1.25722791
X-RAY DIFFRACTIONr_scbond_it2.26431076
X-RAY DIFFRACTIONr_scangle_it3.9084.51009
LS refinement shellResolution: 1.799→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 86 -
Rwork0.216 1948 -
obs--99.56 %
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)
10.5661-0.0511-0.04960.74870.17530.55060.0109-0.02780.06950.0293-0.0044-0.0554-0.06780.0545-0.00640.06910.0067-0.00960.08640.00760.054926.95713.34858.3077
21.2587-0.1352-0.00380.99370.35261.4224-0.01520.0006-0.0061-0.0313-0.05380.1102-0.013-0.13930.0690.0699-0.00120.01170.04710.0410.072323.33590.257630.6321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 300
2X-RAY DIFFRACTION2A301 - 376

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