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- PDB-8zij: The holo structure of gamma-lyase CndF -

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Basic information

Entry
Database: PDB / ID: 8zij
TitleThe holo structure of gamma-lyase CndF
ComponentsPLP dependent gamma-lyase CndF
KeywordsLYASE / PLP dependent / Gamma-lyase / C-C bond formation
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesPenicillium citrinum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsGao, Y. / Tang, Y. / Zhou, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2025
Title: Structure and Mechanism of the Pyridoxal 5'-Phosphate-Dependent Amino Acid gamma-Substitution Enzyme in 6-Alkyl-Pipecolate Biosynthesis
Authors: Gao, Y. / Wang, B. / Zhou, J. / Gu, Y.
History
DepositionMay 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)126,6854
Polymers126,5552
Non-polymers1302
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-42 kcal/mol
Surface area36380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.432, 102.527, 128.124
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 64 through 73 or (resid 74...
d_2ens_1(chain "B" and (resid 64 through 120 or (resid 121...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYPROPROAB64 - 55366 - 555
d_21GLYGLYASPASPBA64 - 25466 - 256
d_22ASPASPALAALABA259 - 510261 - 512
d_23PROPROPROPROBA524 - 553526 - 555

NCS oper: (Code: givenMatrix: (-0.179022052494, 0.953574957459, -0.24216916655), (0.951943019124, 0.105714458208, -0.287452503323), (-0.248506726391, -0.281991584684, -0.926674243252)Vector: -26. ...NCS oper: (Code: given
Matrix: (-0.179022052494, 0.953574957459, -0.24216916655), (0.951943019124, 0.105714458208, -0.287452503323), (-0.248506726391, -0.281991584684, -0.926674243252)
Vector: -26.0146380198, 28.0665423892, 22.162893614)

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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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.22 Å3/Da / Density % sol: 44.72 %
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: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.59→47.6 Å / Num. obs: 35765 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.082 / Net I/σ(I): 9.6
Reflection shellResolution: 2.59→2.71 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.462 / Mean I/σ(I) obs: 2 / Num. unique obs: 4321 / CC1/2: 0.755 / Rpim(I) all: 0.583 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→47.6 Å / SU ML: 0.3516 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9414
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2549 1739 4.87 %
Rwork0.2142 33965 -
obs0.2163 35704 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.5 Å2
Refinement stepCycle: LAST / Resolution: 2.59→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7309 0 21 98 7428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00637497
X-RAY DIFFRACTIONf_angle_d0.783410205
X-RAY DIFFRACTIONf_chiral_restr0.0611153
X-RAY DIFFRACTIONf_plane_restr0.00551319
X-RAY DIFFRACTIONf_dihedral_angle_d14.60492685
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.943164846558 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.670.34551400.28242791X-RAY DIFFRACTION100
2.67-2.750.30941400.27622797X-RAY DIFFRACTION100
2.75-2.850.33051440.2812809X-RAY DIFFRACTION99.93
2.85-2.960.29141520.27682760X-RAY DIFFRACTION100
2.96-3.10.31081310.24762813X-RAY DIFFRACTION100
3.1-3.260.26071530.24072779X-RAY DIFFRACTION100
3.26-3.470.28511390.23762816X-RAY DIFFRACTION100
3.47-3.730.25251280.21482833X-RAY DIFFRACTION100
3.74-4.110.21621550.19372848X-RAY DIFFRACTION100
4.11-4.70.2271440.17942834X-RAY DIFFRACTION100
4.71-5.930.25551590.18942876X-RAY DIFFRACTION100
5.93-47.60.22411540.19063009X-RAY DIFFRACTION99.78

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