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- PDB-5b3a: Crystal Structure of O-Phoshoserine Sulfhydrylase from Aeropyrum ... -

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Basic information

Entry
Database: PDB / ID: 5b3a
TitleCrystal Structure of O-Phoshoserine Sulfhydrylase from Aeropyrum pernix in Complexed with the alpha-Aminoacrylate Intermediate
ComponentsProtein CysO
KeywordsTRANSFERASE / Cysteine Biosynthesis / sulfhydrylase / intermediate / External Schiff base of PLP with alpha-amino acrylate
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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Alpha-Beta Complex / Rossmann fold ...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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0JO / Protein CysO
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.14 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 12, 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 1.3May 10, 2017Group: Non-polymer description
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)84,9206
Polymers84,0522
Non-polymers8694
Water6,269348
1
A: Protein CysO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4603
Polymers42,0261
Non-polymers4342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-9 kcal/mol
Surface area15490 Å2
MethodPISA
2
B: Protein CysO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4603
Polymers42,0261
Non-polymers4342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-5 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.151, 74.151, 275.961
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-0JO / 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid


Mass: 316.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N2O7P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 27% 2-propanol, 12% PEG4000, 12 mM TCEP-HCl, the crystal was soaked with the reservoir solution containing 5% MPD as a cryoprotectant, 20 mM O-phospho-L-serine (OPS) 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: Nov 24, 2009
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: 2.14→32.92 Å / Num. obs: 40639 / % possible obs: 97.99 % / Redundancy: 10 % / Net I/σ(I): 59.8
Reflection shellResolution: 2.14→2.18 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: CysO free form (PDB ID, 3VSA)

3vsa


Resolution: 2.14→32.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.821 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20284 2161 5 %RANDOM
Rwork0.1417 ---
obs0.14471 40639 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.593 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.14→32.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5834 0 58 348 6240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196108
X-RAY DIFFRACTIONr_bond_other_d0.0010.025903
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.9898313
X-RAY DIFFRACTIONr_angle_other_deg0.9643.00213530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9085788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90922.765264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14515991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1441560
X-RAY DIFFRACTIONr_chiral_restr0.1320.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021375
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_it1.8121.7633099
X-RAY DIFFRACTIONr_mcbond_other1.8091.7633092
X-RAY DIFFRACTIONr_mcangle_it2.8212.6363877
X-RAY DIFFRACTIONr_mcangle_other2.8222.6373874
X-RAY DIFFRACTIONr_scbond_it2.5892.0663009
X-RAY DIFFRACTIONr_scbond_other2.5892.0663009
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.112.984423
X-RAY DIFFRACTIONr_long_range_B_refined6.48414.7347253
X-RAY DIFFRACTIONr_long_range_B_other6.40414.5567148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.141→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 163 -
Rwork0.152 2862 -
obs--96.15 %

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