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- PDB-7ysk: Crystal structure of D-Cysteine desulfhydrase from Pectobacterium... -

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Basic information

Entry
Database: PDB / ID: 7ysk
TitleCrystal structure of D-Cysteine desulfhydrase from Pectobacterium atrosepticum
ComponentsD-Cysteine desulfhydrase
KeywordsLYASE / PLP-dependent enzyme / D-Cysteine desulfhydrase / geminal diamine
Function / homologyL-cysteate sulfo-lyase / 1-aminocyclopropane-1-carboxylate deaminase activity / D-cysteine desulfhydrase / D-cysteine desulfhydrase activity / 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / L-cysteate sulfo-lyase
Function and homology information
Biological speciesPectobacterium atrosepticum SCRI1043 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, X. / Wang, L. / Xu, X. / Xing, X. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA09005000 China
CitationJournal: Tetrahedron / Year: 2022
Title: Characterization and structural basis of D-cysteine desulfhydrase from Pectobacterium atrosepticum
Authors: Xu, X. / Yang, L. / Zhang, X. / Xing, X. / Zhou, J.
History
DepositionAug 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: 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

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Assembly

Deposited unit
A: D-Cysteine desulfhydrase
B: D-Cysteine desulfhydrase


Theoretical massNumber of molelcules
Total (without water)79,9302
Polymers79,9302
Non-polymers00
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-14 kcal/mol
Surface area24430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.474, 86.540, 68.482
Angle α, β, γ (deg.)90.000, 90.450, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein D-Cysteine desulfhydrase


Mass: 39965.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum SCRI1043 (bacteria)
Strain: SCRI 1043 / ATCC BAA-672 / Gene: ECA1531 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6D6Z8, D-cysteine desulfhydrase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.77 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG6000, 100 mM MES/sodium hydroxide pH 6.0, 200 mM ammonium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8→44.87 Å / Num. obs: 55529 / % possible obs: 98 % / Redundancy: 5.3 % / Biso Wilson estimate: 17.01 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3320 / CC1/2: 0.764 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D97

4d97


Resolution: 1.8→37.65 Å / SU ML: 0.2429 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1119
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2676 2640 4.91 %
Rwork0.2228 51093 -
obs0.225 53733 94.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.43 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 0 454 5586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00755308
X-RAY DIFFRACTIONf_angle_d0.91417207
X-RAY DIFFRACTIONf_chiral_restr0.0543809
X-RAY DIFFRACTIONf_plane_restr0.0074950
X-RAY DIFFRACTIONf_dihedral_angle_d13.43121971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.40131300.34082788X-RAY DIFFRACTION99.45
1.83-1.870.31221240.31262828X-RAY DIFFRACTION99.39
1.87-1.910.61210.50512229X-RAY DIFFRACTION78.02
1.91-1.950.6008930.52112088X-RAY DIFFRACTION73.98
1.95-1.990.36731520.32422742X-RAY DIFFRACTION98.23
1.99-2.040.28951400.25842801X-RAY DIFFRACTION98.79
2.04-2.10.48881310.39522447X-RAY DIFFRACTION85.65
2.1-2.160.24121360.21422817X-RAY DIFFRACTION99.6
2.16-2.230.25981500.21752751X-RAY DIFFRACTION97.91
2.23-2.310.42151410.32692464X-RAY DIFFRACTION87.62
2.31-2.40.2361440.19932824X-RAY DIFFRACTION98.87
2.4-2.510.26431250.19842783X-RAY DIFFRACTION98.14
2.51-2.640.24881420.20022835X-RAY DIFFRACTION99.87
2.64-2.810.30091560.22572743X-RAY DIFFRACTION97.61
2.81-3.030.21451290.20022828X-RAY DIFFRACTION99.16
3.03-3.330.20861560.19062802X-RAY DIFFRACTION98.04
3.33-3.810.24551530.17842776X-RAY DIFFRACTION97.83
3.81-4.80.17221340.14052765X-RAY DIFFRACTION96.03
4.8-37.650.17841830.14832782X-RAY DIFFRACTION97.18

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