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- PDB-9kq4: The structure of YcfC from Erwinia amylovora as a C-S lyase -

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Basic information

Entry
Database: PDB / ID: 9kq4
TitleThe structure of YcfC from Erwinia amylovora as a C-S lyase
ComponentsYcfC
KeywordsLYASE / PLP dependent C-S lyase / YcfA-YcfC bipartite enzyme system
Function / homologyProtein of unknown function DUF6024 / Family of unknown function (DUF6024) / Uncharacterized protein
Function and homology information
Biological speciesErwinia amylovora ATCC 49946 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsZhang, L. / Dou, C. / Zheng, Y.H. / Zhu, X.F. / Cheng, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32225001 China
National Natural Science Foundation of China (NSFC)32200114 China
CitationJournal: Nat Commun / Year: 2025
Title: The mechanism of thioamide formation by the YcfA-YcfC system in 6-thioguanine biosynthesis.
Authors: Zhang, L. / Dou, C. / Yan, W. / Chen, P. / Jia, X. / Zhang, N. / Zhou, D. / Long, Z. / Zhang, L. / Zhu, X. / Cheng, W.
History
DepositionNov 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YcfC
B: YcfC


Theoretical massNumber of molelcules
Total (without water)65,6802
Polymers65,6802
Non-polymers00
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-25 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.619, 152.619, 73.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

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Components

#1: Protein YcfC


Mass: 32840.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Erwinia amylovora ATCC 49946 is not available during the biocuration, replaced by A0A831A010 temporarily.
Source: (gene. exp.) Erwinia amylovora ATCC 49946 (bacteria)
Gene: BN437_1049 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A831A010
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 50 mM sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→41.8 Å / Num. obs: 50350 / % possible obs: 93.38 % / Redundancy: 20 % / Rpim(I) all: 0.04886 / Net I/σ(I): 14.67
Reflection shellResolution: 2.09→2.142 Å / Num. unique obs: 4237 / CC1/2: 0.844

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→41.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.867 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1913 3.9 %RANDOM
Rwork0.1847 ---
obs-48272 93.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.375 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å2-0 Å2-0 Å2
2--1.87 Å2-0 Å2
3----3.73 Å2
Refinement stepCycle: 1 / Resolution: 2.09→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4523 0 30 355 4908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0124659
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164335
X-RAY DIFFRACTIONr_angle_refined_deg2.4691.8226321
X-RAY DIFFRACTIONr_angle_other_deg0.8711.7559997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9295569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.4532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47310784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1260.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025463
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021075
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.0943.8072288
X-RAY DIFFRACTIONr_mcbond_other6.0913.8052287
X-RAY DIFFRACTIONr_mcangle_it7.7716.8072853
X-RAY DIFFRACTIONr_mcangle_other7.7696.8092854
X-RAY DIFFRACTIONr_scbond_it7.8364.3422371
X-RAY DIFFRACTIONr_scbond_other7.844.3432368
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.7727.6673469
X-RAY DIFFRACTIONr_long_range_B_refined12.91938.395371
X-RAY DIFFRACTIONr_long_range_B_other12.88138.025247
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.142 Å
RfactorNum. reflection% reflection
Rfree0.294 119 -
Rwork0.281 3032 -
obs--83.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0324-0.0590.04220.2628-0.51451.33120.00310.00990.0427-0.0932-0.0006-0.05270.2054-0.0727-0.00250.0536-0.0075-0.00570.01530.01010.0691-51.271422.3706-22.0637
20.0963-0.11410.19770.1475-0.19171.4492-0.0304-0.03080.02290.02560.0126-0.03570.0467-0.0940.01780.01560.0099-0.00940.03010.00520.0514-52.348623.90517.9383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 301
2X-RAY DIFFRACTION2B1 - 301

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