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- PDB-6l0r: Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aerop... -

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Basic information

Entry
Database: PDB / ID: 6l0r
TitleCrystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed with O-Acetylserine
ComponentsProtein CysO
KeywordsTRANSFERASE / CYSTEINE BIOSYNTHESIS / SULFHYDRYLASE
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
Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
Chem-E1R / Protein CysO
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsNakabayashi, M. / Takeda, E. / Ishikawa, K. / Nakamura, T.
CitationJournal: J.Biosci.Bioeng. / Year: 2021
Title: Identification of amino acid residues important for recognition of O-phospho-l-serine substrates by cysteine synthase.
Authors: Takeda, E. / Matsui, E. / Kiryu, T. / Nakagawa, T. / Nakabayashi, M. / Ishikawa, K. / Nakamura, T.
History
DepositionSep 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 12, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)169,33210
Polymers167,5914
Non-polymers1,7416
Water1,20767
1
A: Protein CysO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3923
Polymers41,8981
Non-polymers4942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-9 kcal/mol
Surface area15800 Å2
MethodPISA
2
B: Protein CysO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2742
Polymers41,8981
Non-polymers3761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15580 Å2
MethodPISA
3
C: Protein CysO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3923
Polymers41,8981
Non-polymers4942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15690 Å2
MethodPISA
4
D: Protein CysO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2742
Polymers41,8981
Non-polymers3761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-8 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.460, 74.460, 275.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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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: 41897.637 Da / Num. of mol.: 4 / Mutation: K127A, F225Y, R297A
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
References: UniProt: Q9YBL2, cystathionine beta-synthase, cysteine synthase, O-phosphoserine sulfhydrylase
#2: Chemical
ChemComp-E1R / (2S)-3-acetyloxy-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]propanoic acid


Mass: 376.256 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H17N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium N-2-hydroxyethylpiperazine-N'-2-ethanesulfonate buffer, pH 8.2 (7.9), 29% (v/v) 2-propanol, 13% (11%) (v/v) polyethylene glycol 4,000, and 11 mM TCEP-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.79→74.46 Å / Num. obs: 139467 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 6.7
Reflection shellResolution: 1.79→1.89 Å / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 20355

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B3A

5b3a


Resolution: 1.79→74.46 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1701 / WRfactor Rwork: 0.163 / FOM work R set: 0.951 / SU B: 1.127 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0988 / SU Rfree: 0.0816 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1498 6914 5 %RANDOM
Rwork0.1454 ---
obs0.1457 132444 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.46 Å2 / Biso mean: 24.612 Å2 / Biso min: 6.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.79→74.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11624 0 116 67 11807
Biso mean--38.06 45.99 -
Num. residues----1528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911978
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211546
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.98716276
X-RAY DIFFRACTIONr_angle_other_deg1.0713.00126486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33551524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38222.937504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.816151908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8415108
X-RAY DIFFRACTIONr_chiral_restr0.0970.21832
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113596
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022664
LS refinement shellResolution: 1.794→1.841 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 550 -
Rwork0.227 9783 -
all-10333 -
obs--99.96 %

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