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- PDB-5b36: Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aerop... -

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Basic information

Entry
Database: PDB / ID: 5b36
TitleCrystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed with Cysteine
ComponentsProtein CysO
KeywordsTRANSFERASE / Cysteine Biosynthesis / sulfhydrylase / complex with L-cysteine
Function / homology
Function and homology information


O-phosphoserine sulfhydrylase / O-phosphoserine sulfhydrylase activity / cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine
Similarity search - Function
Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain - #20 / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Alpha-Beta Complex ...Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain - #20 / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYSTEINE / PYRIDOXAL-5'-PHOSPHATE / Protein CysO
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsNakamura, T. / Takeda, E. / Kawai, Y. / Kataoka, M. / Ishikawa, K.
Citation
Journal: Extremophiles / Year: 2016
Title: Role of F225 in O-phosphoserine sulfhydrylase from Aeropyrum pernix K1
Authors: Takeda, E. / Kunimoto, K. / Kawai, Y. / Kataoka, M. / Ishikawa, K. / Nakamura, T.
#1: Journal: J.Mol.Biol. / Year: 2012
Title: Structural analysis of the substrate recognition mechanism in O-phosphoserine sulfhydrylase from the hyperthermophilic archaeon Aeropyrum pernix K1
Authors: Nakamura, T. / Kawai, Y. / Kunimoto, K. / Iwasaki, Y. / Nishii, K. / Kataoka, M. / Ishikawa, K.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Three-dimensional structure of a new enzyme, O-phosphoserine sulfhydrylase, involved in l-cysteine biosynthesis by a hyperthermophilic archaeon, Aeropyrum pernix K1, at 2.0A resolution
Authors: Oda, Y. / Mino, K. / Ishikawa, K. / Ataka, M.
History
DepositionFeb 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein CysO
B: Protein CysO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9067
Polymers84,0522
Non-polymers8555
Water4,828268
1
A: Protein CysO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5124
Polymers42,0261
Non-polymers4863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-9 kcal/mol
Surface area15720 Å2
MethodPISA
2
B: Protein CysO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3943
Polymers42,0261
Non-polymers3682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-0 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.181, 74.181, 278.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein CysO / Cystathionine beta-synthase / Cysteine synthase / O-acetylserine sulfhydrylase / O-phosphoserine ...Cystathionine beta-synthase / Cysteine synthase / O-acetylserine sulfhydrylase / O-phosphoserine sulfhydrylase / Serine sulfhydrase


Mass: 42025.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Strain: K1 / Gene: cysO, APE_1586 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: Q9YBL2, cystathionine beta-synthase, cysteine synthase, O-phosphoserine sulfhydrylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 27% 2-propanol, 10% PEG4000, 12 mM TCEP-HCl, the crystal was soaked with the reservoir solution containing 6% MPD as a cryoprotectant, 20 mM L-cysteine, and 12 mM TCEP-HCl

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jan 29, 2010
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.15→49.1 Å / Num. obs: 43621 / % possible obs: 92 % / Redundancy: 13.5 % / Net I/σ(I): 17
Reflection shellResolution: 2.14→2.18 Å

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: CysO free form (PDB ID, 3VSA)

3vsa


Resolution: 2.15→49.1 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.615 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.224 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24598 1991 5 %RANDOM
Rwork0.18017 ---
obs0.18335 38060 92.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 36.235 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.15→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5834 0 52 268 6154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0226090
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0911.9868277
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9385779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59422.71262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38615988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2861560
X-RAY DIFFRACTIONr_chiral_restr0.2230.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214674
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1681.53854
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07726191
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.40932236
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3384.52086
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.152→2.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 118 -
Rwork0.249 2566 -
obs--85.53 %

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