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

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Basic information

Entry
Database: PDB / ID: 2zyf
TitleCrystal structure of homocitrate synthase from Thermus thermophilus complexed with magnesuim ion and alpha-ketoglutarate
ComponentsHomocitrate synthase
KeywordsTRANSFERASE / TIM barrel / 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 / Homocitrate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsOkada, T. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
CitationJournal: J.Biol.Chem. / Year: 2009
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
DepositionJan 20, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 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_ref_seq_dif / 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_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)43,2443
Polymers43,0741
Non-polymers1702
Water2,558142
1
A: Homocitrate synthase
hetero molecules

A: Homocitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4896
Polymers86,1482
Non-polymers3414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area6050 Å2
ΔGint-27 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.465, 135.465, 126.612
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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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-hcs / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus-RIL (DE3) / References: UniProt: O87198, homocitrate synthase
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.89 Å3/Da / Density % sol: 68.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES-NaOH (pH6.0), 1.6M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 37714 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 40.8
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3683 / Rsym value: 0.546 / % 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: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZTJ

2ztj


Resolution: 2.15→31.51 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.686 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23152 1882 5 %RANDOM
Rwork0.2033 ---
obs0.20469 35766 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.582 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→31.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 11 142 2616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222563
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9713478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59523.223121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84715446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9531525
X-RAY DIFFRACTIONr_chiral_restr0.1010.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021958
X-RAY DIFFRACTIONr_nbd_refined0.2220.21233
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.214
X-RAY DIFFRACTIONr_mcbond_it0.8221.51640
X-RAY DIFFRACTIONr_mcangle_it1.28622560
X-RAY DIFFRACTIONr_scbond_it2.0331043
X-RAY DIFFRACTIONr_scangle_it3.2984.5912
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 122 -
Rwork0.287 2554 -
obs--98.89 %

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