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- PDB-9k3c: Crystal Structure of CapA2 from Alistipes finegoldii in complex w... -

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Basic information

Entry
Database: PDB / ID: 9k3c
TitleCrystal Structure of CapA2 from Alistipes finegoldii in complex with PLP cofactor
ComponentsCysteate synthase
KeywordsBIOSYNTHETIC PROTEIN / PLP-dependent enzyme
Function / homologyCysteate synthase / coenzyme M biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / CITRIC ACID / PYRIDOXAL-5'-PHOSPHATE / Cysteate synthase
Function and homology information
Biological speciesAlistipes finegoldii DSM 17242 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsYang, S. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal Structure of CapA2 from Alistipes finegoldii in complex with PLP cofactor
Authors: Zhang, Y. / Yang, S.
History
DepositionOct 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3453
Polymers47,9061
Non-polymers4392
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, monomer is verified by through out of size exclusion chromatography calibrated
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.821, 88.511, 95.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cysteate synthase


Mass: 47905.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alistipes finegoldii DSM 17242 (bacteria)
Gene: Alfi_3017 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3YQJ3
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: sodium citrate, PEG8000

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Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.38→30.39 Å / Num. obs: 23687 / % possible obs: 98.98 % / Redundancy: 5.66 % / CC1/2: 0.876 / Net I/σ(I): 5.8
Reflection shellResolution: 2.38→2.465 Å / Num. unique obs: 43738 / CC1/2: 0.876

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
xia2data reduction
PHENIXphasing
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→29.848 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 0 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1936 8.37 %
Rwork0.1817 --
obs0.1857 23144 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→29.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 13 153 3508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083419
X-RAY DIFFRACTIONf_angle_d0.8864629
X-RAY DIFFRACTIONf_dihedral_angle_d6.4552037
X-RAY DIFFRACTIONf_chiral_restr0.047501
X-RAY DIFFRACTIONf_plane_restr0.006597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3801-2.43960.29481270.25091287X-RAY DIFFRACTION84
2.4396-2.50550.29131220.22951370X-RAY DIFFRACTION90
2.5055-2.57920.27451200.22451476X-RAY DIFFRACTION95
2.5792-2.66240.26811500.21981490X-RAY DIFFRACTION96
2.6624-2.75750.26671260.21331514X-RAY DIFFRACTION98
2.7575-2.86780.30661530.21519X-RAY DIFFRACTION98
2.8678-2.99820.2111280.18681525X-RAY DIFFRACTION98
2.9982-3.15620.24961460.18371525X-RAY DIFFRACTION99
3.1562-3.35370.22191450.1771530X-RAY DIFFRACTION99
3.3537-3.61220.21341330.16691566X-RAY DIFFRACTION99
3.6122-3.97490.21371430.15571565X-RAY DIFFRACTION100
3.9749-4.54840.19131530.14361572X-RAY DIFFRACTION100
4.5484-5.72390.18881400.16221598X-RAY DIFFRACTION100
5.7239-29.8480.19361500.17691671X-RAY DIFFRACTION99

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