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- PDB-3vsd: Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydr... -

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Basic information

Entry
Database: PDB / ID: 3vsd
TitleCrystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Acetyl-L-Serine
ComponentsProtein CysO
KeywordsTRANSFERASE / Cysteine Biosynthesis / External Schiff base of PLP with O-acetylserine / K127A mutant / Sulfhydrylase (inactivated)
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
O-ACETYLSERINE / PYRIDOXAL-5'-PHOSPHATE / Protein CysO
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.09 Å
AuthorsNakamura, T. / Kawai, Y. / Kataoka, M. / Ishikawa, K.
Citation
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.
#1: 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
DepositionApr 24, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,8427
Polymers83,9362
Non-polymers9075
Water1,78399
1
A: Protein CysO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4804
Polymers41,9681
Non-polymers5123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein CysO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3623
Polymers41,9681
Non-polymers3942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-46 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.646, 75.646, 275.784
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 41967.754 Da / Num. of mol.: 2 / Mutation: K127A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: APE1586, APE_1586, cysO / 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 / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-OAS / O-ACETYLSERINE / O-Acetylserine


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 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 / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.35 Å3/Da / Density % sol: 47.66 % / Mosaicity: 0.751 °
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M HEPES sodium pH 6.8, 27% 2-propanol, 10% PEG 4000, 5mM O-acetyl-L-serine, 5mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jul 9, 2009 / Details: rhodium-coated mirror (horizontal)
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 47287 / % possible obs: 97.7 % / Redundancy: 7.8 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.08 / Χ2: 0.983 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.09-2.143.80.33522320.509195.1
2.14-2.184.20.29723070.54196.3
2.18-2.224.50.27922760.565197.5
2.22-2.264.70.26123200.555197.5
2.26-2.315.10.26823190.6197.8
2.31-2.375.40.25823250.604197.6
2.37-2.425.70.24123150.626197.2
2.42-2.496.10.21123300.663197.7
2.49-2.566.50.19923280.711197.9
2.56-2.6570.19323310.753198
2.65-2.747.30.17523560.804198
2.74-2.857.70.15623530.875198.1
2.85-2.988.40.13323690.946198.1
2.98-3.149.40.11723611.059197.8
3.14-3.339.90.10423661.176197.4
3.33-3.5910.60.0923901.062198
3.59-3.9511.70.07724071.088198
3.95-4.5211.80.06824281.326198.1
4.52-5.712.20.05924801.182198.3
5.7-50120.05526941.511198.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.09→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2766 / WRfactor Rwork: 0.2038 / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.763 / SU B: 8.259 / SU ML: 0.206 / SU R Cruickshank DPI: 0.27 / SU Rfree: 0.2399 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3047 2386 5 %RANDOM
Rwork0.2333 ---
obs0.2367 47256 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.31 Å2 / Biso mean: 44.646 Å2 / Biso min: 14.25 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å20 Å2
2--2.43 Å20 Å2
3----4.85 Å2
Refinement stepCycle: LAST / Resolution: 2.09→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5826 0 58 99 5983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226052
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.9888227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3375773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86922.791258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.43315971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7281558
X-RAY DIFFRACTIONr_chiral_restr0.1250.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214642
X-RAY DIFFRACTIONr_mcbond_it0.9421.53836
X-RAY DIFFRACTIONr_mcangle_it1.66126157
X-RAY DIFFRACTIONr_scbond_it2.64632216
X-RAY DIFFRACTIONr_scangle_it4.1314.52070
LS refinement shellResolution: 2.094→2.148 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 181 -
Rwork0.45 3092 -
all-3273 -
obs--93.38 %

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