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- PDB-7yeo: Crystal Structure of cystathionine gamma-synthase-like protein C2... -

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Basic information

Entry
Database: PDB / ID: 7yeo
TitleCrystal Structure of cystathionine gamma-synthase-like protein C23A1.14c
ComponentsUncharacterized trans-sulfuration enzyme C23A1.14c
KeywordsHYDROLASE / cystathionine gamma-synthase-like protein
Function / homology
Function and homology information


Degradation of cysteine and homocysteine / Cysteine formation from homocysteine / carbon-sulfur lyase activity / transsulfuration / pyridoxal phosphate binding / transferase activity / cytoplasm
Similarity search - Function
Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Uncharacterized trans-sulfuration enzyme C23A1.14c
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhang, S.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal Structure of cystathionine gamma-synthase-like protein C23A1.14c
Authors: Zhang, S.J.
History
DepositionJul 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized trans-sulfuration enzyme C23A1.14c
B: Uncharacterized trans-sulfuration enzyme C23A1.14c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2116
Polymers86,6682
Non-polymers5434
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-40 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.390, 106.820, 82.810
Angle α, β, γ (deg.)90.000, 128.000, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Uncharacterized trans-sulfuration enzyme C23A1.14c


Mass: 43334.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: SPAC23A1.14c / Production host: Escherichia coli (E. coli) / References: UniProt: O42851
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: peg550, HEPES, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.7→27.15 Å / Num. obs: 87191 / % possible obs: 98.75 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07372 / Net I/σ(I): 15.21
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.8958 / Mean I/σ(I) obs: 2.87 / Num. unique obs: 8664 / CC1/2: 0.829 / Rpim(I) all: 0.3564 / % possible all: 98.01

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3e6g

3e6g


Resolution: 1.7→27.15 Å / SU ML: 0.1685 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1857 4417 5.07 %
Rwork0.1612 82764 -
obs0.1624 87181 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.68 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5857 0 32 489 6378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01176103
X-RAY DIFFRACTIONf_angle_d1.40578325
X-RAY DIFFRACTIONf_chiral_restr0.0911970
X-RAY DIFFRACTIONf_plane_restr0.00961062
X-RAY DIFFRACTIONf_dihedral_angle_d18.08962187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.27611460.23132727X-RAY DIFFRACTION97.95
1.72-1.740.27551530.2322694X-RAY DIFFRACTION97.94
1.74-1.760.26311650.23442778X-RAY DIFFRACTION98.17
1.76-1.780.28251330.22072671X-RAY DIFFRACTION98.01
1.78-1.810.2691490.22992795X-RAY DIFFRACTION98.26
1.81-1.830.25331290.2082718X-RAY DIFFRACTION98.27
1.83-1.860.20761420.20812741X-RAY DIFFRACTION98.53
1.86-1.890.22371750.19212736X-RAY DIFFRACTION98.44
1.89-1.910.20311440.18182727X-RAY DIFFRACTION98.42
1.91-1.950.21831510.18392736X-RAY DIFFRACTION98.57
1.95-1.980.22071640.18662749X-RAY DIFFRACTION98.65
1.98-2.020.22071470.18172759X-RAY DIFFRACTION98.78
2.02-2.050.21931550.18242721X-RAY DIFFRACTION98.59
2.05-2.10.20311510.17492760X-RAY DIFFRACTION99.05
2.1-2.140.22281370.17132763X-RAY DIFFRACTION98.98
2.14-2.190.21391350.16762744X-RAY DIFFRACTION98.7
2.19-2.250.19271490.16922781X-RAY DIFFRACTION99.02
2.25-2.310.19461360.16992764X-RAY DIFFRACTION98.77
2.31-2.370.18661450.16612758X-RAY DIFFRACTION99.18
2.37-2.450.18741520.16322756X-RAY DIFFRACTION99.01
2.45-2.540.1761380.16632767X-RAY DIFFRACTION99.11
2.54-2.640.17411280.16322810X-RAY DIFFRACTION99.16
2.64-2.760.19971590.16392758X-RAY DIFFRACTION99.12
2.76-2.910.20831520.16812759X-RAY DIFFRACTION99.22
2.91-3.090.19421550.16072772X-RAY DIFFRACTION99.12
3.09-3.330.19181560.16122764X-RAY DIFFRACTION99.12
3.33-3.660.17061460.14252781X-RAY DIFFRACTION98.89
3.66-4.190.14351370.13572819X-RAY DIFFRACTION99.43
4.19-5.270.1341450.12792804X-RAY DIFFRACTION99.46
5.27-27.150.16131430.1532852X-RAY DIFFRACTION99.53

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