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- PDB-2ecq: Crystal Structure of T.th. HB8 O-acetylserine sulfhydrylase Compl... -

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Basic information

Entry
Database: PDB / ID: 2ecq
TitleCrystal Structure of T.th. HB8 O-acetylserine sulfhydrylase Complexed with 3-Hydroxylactate
ComponentsO-acetylserine (Thiol)-lyase
KeywordsTRANSFERASE / PLP-dependent
Function / homology
Function and homology information


cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(3S)-3-HYDROXYBUTANOIC ACID / PYRIDOXAL-5'-PHOSPHATE / Cysteine synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGoto, M.
CitationJournal: to be published
Title: Crystal Structure of T.th. HB8 O-acetylserine sulfhydrylase Complexed with 3-Hydroxylactate
Authors: Goto, M.
History
DepositionFeb 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: O-acetylserine (Thiol)-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4163
Polymers33,0651
Non-polymers3512
Water6,053336
1
A: O-acetylserine (Thiol)-lyase
hetero molecules

A: O-acetylserine (Thiol)-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8336
Polymers66,1302
Non-polymers7024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area4910 Å2
ΔGint-23 kcal/mol
Surface area21840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.531, 104.531, 79.802
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein O-acetylserine (Thiol)-lyase / O-acetylserine sulfhydrylase / Cysteine synthase


Mass: 33065.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RP / References: UniProt: Q5SLE6, cysteine synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-3HL / (3S)-3-HYDROXYBUTANOIC ACID


Mass: 104.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 3.8 Å3/Da / Density % sol: 67.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium Sulfate, Tris-HCl, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 22, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→45.26 Å / Num. all: 39981 / Num. obs: 37594 / % possible obs: 93.8 % / Biso Wilson estimate: 16.5 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 79.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VE1

1ve1


Resolution: 1.9→39.37 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1742599.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2 3764 10 %RANDOM
Rwork0.179 ---
obs0.179 37594 93.9 %-
all-39981 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.2874 Å2 / ksol: 0.385086 e/Å3
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.63 Å20 Å2
3---1.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 22 336 2650
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it21.462
X-RAY DIFFRACTIONc_scangle_it10.932.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 585 10.6 %
Rwork0.216 4929 -
obs--83.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwat.top
X-RAY DIFFRACTION33hl.param3hl.top
X-RAY DIFFRACTION4plp.paramplp.top
X-RAY DIFFRACTION5etc.paramintshiff.top

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