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- PDB-9k3o: Crystal structure of CapA2 from Alistipes finegoldii in complex w... -

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Basic information

Entry
Database: PDB / ID: 9k3o
TitleCrystal structure of CapA2 from Alistipes finegoldii in complex with OPS-PLP external aldimine
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 / Chem-E1U / Cysteate synthase
Function and homology information
Biological speciesAlistipes finegoldii DSM 17242 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 OPS-PLP external aldimine
Authors: Yang, S. / Zhang, Y.
History
DepositionOct 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 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)48,3202
Polymers47,9061
Non-polymers4141
Water10,701594
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Throughout proved the monomer status of protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.550, 88.460, 95.950
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
Details: PLP-dependent enzyme bound with OPS-PLP external aldimine
Source: (gene. exp.) Alistipes finegoldii DSM 17242 (bacteria)
Gene: Alfi_3017 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3YQJ3
#2: Chemical ChemComp-E1U / (2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic acid


Mass: 414.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging 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: May 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.43→65.03 Å / Num. obs: 107058 / % possible obs: 98.97 % / Redundancy: 6.2 % / CC1/2: 0.8 / Net I/σ(I): 17
Reflection shellResolution: 1.43→1.481 Å / Num. unique obs: 205467 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→34.275 Å / SU ML: 0.08 / Cross valid method: NONE / σ(F): 0 / Phase error: 15.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1716 1989 1.87 %
Rwork0.1567 --
obs0.157 106287 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.43→34.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 0 594 3946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053428
X-RAY DIFFRACTIONf_angle_d0.9234644
X-RAY DIFFRACTIONf_dihedral_angle_d3.9431245
X-RAY DIFFRACTIONf_chiral_restr0.081502
X-RAY DIFFRACTIONf_plane_restr0.005599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.46580.21841240.20616408X-RAY DIFFRACTION86
1.4658-1.50540.17951310.19087159X-RAY DIFFRACTION95
1.5054-1.54970.19271400.1767394X-RAY DIFFRACTION98
1.5497-1.59970.17831440.15927395X-RAY DIFFRACTION98
1.5997-1.65690.16611540.15037430X-RAY DIFFRACTION99
1.6569-1.72320.15381170.15057506X-RAY DIFFRACTION99
1.7232-1.80160.17281530.15447502X-RAY DIFFRACTION100
1.8016-1.89660.18381560.15747508X-RAY DIFFRACTION100
1.8966-2.01540.15931270.15437583X-RAY DIFFRACTION100
2.0154-2.1710.17821520.15187542X-RAY DIFFRACTION100
2.171-2.38950.18271460.15537605X-RAY DIFFRACTION100
2.3895-2.73510.17381450.16527630X-RAY DIFFRACTION100
2.7351-3.44540.17271430.15897705X-RAY DIFFRACTION100
3.4454-34.2750.1591570.14557931X-RAY DIFFRACTION100

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