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- PDB-8zif: Gamma-lyase CndF in complex with pyridoxal 5'-phosphate, L-homose... -

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Basic information

Entry
Database: PDB / ID: 8zif
TitleGamma-lyase CndF in complex with pyridoxal 5'-phosphate, L-homoserine and ethyl acetoacetate
ComponentsPLP dependent gamma-lyase CndF
KeywordsLYASE / PLP dependent / Gamma-lyase / C-C bond formation
Function / homologyethyl 3-oxobutanoate / L-HOMOSERINE
Function and homology information
Biological speciesPenicillium citrinum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsGao, Y. / Zhou, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Gamma-lyase CndF in complex with pyridoxal 5'-phosphate, L-homoserine and ethyl acetoacetate
Authors: Gao, Y. / Zhou, J.
History
DepositionMay 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLP dependent gamma-lyase CndF
B: PLP dependent gamma-lyase CndF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8044
Polymers126,5552
Non-polymers2492
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.709, 100.650, 129.076
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein PLP dependent gamma-lyase CndF


Mass: 63277.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence matches GenBank Code KAK5801372.1, except for two mismatches (F15L and L561F).
Source: (gene. exp.) Penicillium citrinum (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-HSE / L-HOMOSERINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EAC / ethyl 3-oxobutanoate


Mass: 130.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O3 / Feature type: SUBJECT OF INVESTIGATION
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: 2.22 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M sodium sulfate, 0.1M Bis-Tris propane pH 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 23658 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 80.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.047 / Net I/σ(I): 18.7
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.624 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1705 / CC1/2: 0.519 / Rpim(I) all: 0.461 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPXdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→46.89 Å / SU ML: 0.4084 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.265 1160 4.93 %
Rwork0.2379 22360 -
obs0.2393 23520 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.6 Å2
Refinement stepCycle: LAST / Resolution: 2.95→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7163 0 47 0 7210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00977377
X-RAY DIFFRACTIONf_angle_d1.199510033
X-RAY DIFFRACTIONf_chiral_restr0.06861132
X-RAY DIFFRACTIONf_plane_restr0.00821290
X-RAY DIFFRACTIONf_dihedral_angle_d14.05212637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.080.36461520.31962721X-RAY DIFFRACTION98.9
3.08-3.250.4091390.33152749X-RAY DIFFRACTION99.07
3.25-3.450.31451430.28022731X-RAY DIFFRACTION99.38
3.45-3.720.24971410.25542779X-RAY DIFFRACTION99.76
3.72-4.090.2791430.24992781X-RAY DIFFRACTION99.86
4.09-4.680.2551380.21982821X-RAY DIFFRACTION99.9
4.68-5.90.24871470.22462826X-RAY DIFFRACTION99.97
5.9-46.890.22211570.20532952X-RAY DIFFRACTION99.87

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