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- PDB-9ns6: KslB apoenzyme -

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Basic information

Entry
Database: PDB / ID: 9ns6
TitleKslB apoenzyme
ComponentsPictet-Spenglerase
KeywordsBIOSYNTHETIC PROTEIN / Pictet-Spenglerase
Function / homologyCucumopine synthase, C-terminal helical bundle domain / Cucumopine synthase C-terminal helical bundle domain / Cucumopine synthase C-terminal helical bundle domain-containing protein
Function and homology information
Biological speciesKitasatospora setae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsKim, K. / Kim, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA281106 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM148356 United States
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Structural and mechanistic insights into KslB, a bacterial Pictet-Spenglerase in kitasetaline biosynthesis.
Authors: Kim, W. / Zheng, Z. / Kim, K. / Lee, Y.H. / Liu, H.W. / Zhang, Y.J.
History
DepositionMar 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pictet-Spenglerase
B: Pictet-Spenglerase
C: Pictet-Spenglerase
D: Pictet-Spenglerase
E: Pictet-Spenglerase
F: Pictet-Spenglerase


Theoretical massNumber of molelcules
Total (without water)211,0706
Polymers211,0706
Non-polymers00
Water00
1
A: Pictet-Spenglerase
B: Pictet-Spenglerase


Theoretical massNumber of molelcules
Total (without water)70,3572
Polymers70,3572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-37 kcal/mol
Surface area21070 Å2
MethodPISA
2
C: Pictet-Spenglerase
D: Pictet-Spenglerase


Theoretical massNumber of molelcules
Total (without water)70,3572
Polymers70,3572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-43 kcal/mol
Surface area20760 Å2
MethodPISA
3
E: Pictet-Spenglerase
F: Pictet-Spenglerase


Theoretical massNumber of molelcules
Total (without water)70,3572
Polymers70,3572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-40 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.593, 95.593, 193.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein
Pictet-Spenglerase / Cucumopine synthase C-terminal helical bundle domain-containing protein


Mass: 35178.398 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora setae (bacteria) / Gene: KSE_70640 / Production host: Escherichia coli (E. coli) / References: UniProt: E4NIM4
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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 3350, Sodium Chloride, bisTRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.49
ReflectionResolution: 2.95→47.8 Å / Num. obs: 40480 / % possible obs: 97.2 % / Redundancy: 2.6 % / CC1/2: 0.972 / Net I/σ(I): 5.2
Reflection shellResolution: 2.95→3 Å / Num. unique obs: 2058 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→47.8 Å / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.404
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2478 2057 5.13 %
Rwork0.2068 38002 -
obs0.2159 40059 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.72 Å2
Refinement stepCycle: LAST / Resolution: 2.95→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13615 0 0 0 13615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011713971
X-RAY DIFFRACTIONf_angle_d1.267619138
X-RAY DIFFRACTIONf_chiral_restr0.0912187
X-RAY DIFFRACTIONf_plane_restr0.02372467
X-RAY DIFFRACTIONf_dihedral_angle_d16.23015031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.020.2911440.25612661X-RAY DIFFRACTION89.3
3.02-3.110.30051440.24812698X-RAY DIFFRACTION91.09
3.11-3.20.29421410.23952709X-RAY DIFFRACTION90.54
3.2-3.30.29551430.23962701X-RAY DIFFRACTION90.55
3.3-3.420.28361300.23632541X-RAY DIFFRACTION85.24
3.42-3.550.30821350.22722661X-RAY DIFFRACTION89.81
3.55-3.720.2891500.21352771X-RAY DIFFRACTION93.71
3.72-3.910.30181500.20812765X-RAY DIFFRACTION93.73
3.91-4.160.24091490.20052847X-RAY DIFFRACTION93.9
4.16-4.480.22811510.19652758X-RAY DIFFRACTION93.4
4.48-4.930.21061510.17992750X-RAY DIFFRACTION93.22
4.93-5.640.19791420.19862763X-RAY DIFFRACTION92.07
5.64-7.10.24621260.2212596X-RAY DIFFRACTION87.85
7.1-47.80.21371520.21862830X-RAY DIFFRACTION94.9

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