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- PDB-7ysl: Crystal structure of D-Cysteine desulfhydrase with a trapped PLP-... -

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Basic information

Entry
Database: PDB / ID: 7ysl
TitleCrystal structure of D-Cysteine desulfhydrase with a trapped PLP-pyruvate geminal diamine
ComponentsD-Cysteine desulfhydrase
KeywordsLYASE / PLP-dependent enzyme / D-Cysteine desulfhydrase / geminal diamine
Function / homology
Function and homology information


1-aminocyclopropane-1-carboxylate deaminase / 1-aminocyclopropane-1-carboxylate deaminase activity / D-cysteine desulfhydrase activity
Similarity search - Function
D-cysteine desulfhydrase / 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme
Similarity search - Domain/homology
FORMIC ACID / 1-aminocyclopropane-1-carboxylate deaminase
Similarity search - Component
Biological speciesPectobacterium atrosepticum SCRI1043 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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 2.0Feb 8, 2023Group: Atomic model / Derived calculations / Category: atom_site / struct_conf
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length
Revision 3.0Nov 29, 2023Group: Data collection / Polymer sequence ...Data collection / Polymer sequence / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity_poly / pdbx_initial_refinement_model
Item: _chem_comp.name / _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,84317
Polymers80,1042
Non-polymers73915
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-7 kcal/mol
Surface area24020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.380, 85.478, 123.091
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-Cysteine desulfhydrase


Mass: 40052.246 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: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Carboxylic acids (sodium formate, ammonium acetate, sodium citrate, potassium sodium tartrate, sodium oxamate), 0.1 M imidazole/MES pH 6.5, 30% (v/v) PEG 500 MME/PEG 20000

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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 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.02→123.09 Å / Num. obs: 46857 / % possible obs: 97.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 28.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Net I/σ(I): 13
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 7 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3518 / CC1/2: 0.746 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D97

4d97


Resolution: 2.02→70.21 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 2180 4.66 %
Rwork0.1718 44583 -
obs0.1735 46763 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101 Å2 / Biso mean: 31.1538 Å2 / Biso min: 15.19 Å2
Refinement stepCycle: final / Resolution: 2.02→70.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 0 48 311 5511
Biso mean--48.15 36.4 -
Num. residues----676
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.02-2.060.27911380.230128262964100
2.06-2.110.28091420.226628042946100
2.11-2.160.27981330.201828142947100
2.16-2.220.20911460.186228102956100
2.22-2.290.27981230.19752225234879
2.29-2.360.21741230.176228532976100
2.36-2.450.22181400.178328182958100
2.45-2.550.25431160.181328592975100
2.55-2.660.21271210.178928552976100
2.66-2.80.2321400.178828432983100
2.8-2.980.19591420.167428542996100
2.98-3.210.24621420.171428552997100
3.21-3.530.17611460.164628813027100
3.53-4.040.17211210.15492338245981
4.04-5.090.18321540.140728953049100
5.09-70.210.19521530.18143053320699

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