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- PDB-9nsu: Bacterial Pictet-Spenglerase KslB in complex with product of L-Tr... -

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Basic information

Entry
Database: PDB / ID: 9nsu
TitleBacterial Pictet-Spenglerase KslB in complex with product of L-Trp and succinic semialdehyde
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: 2.87 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 17, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,80012
Polymers211,0706
Non-polymers1,7306
Water00
1
A: Pictet-Spenglerase
B: Pictet-Spenglerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9334
Polymers70,3572
Non-polymers5772
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-51 kcal/mol
Surface area20710 Å2
MethodPISA
2
C: Pictet-Spenglerase
D: Pictet-Spenglerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9334
Polymers70,3572
Non-polymers5772
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-50 kcal/mol
Surface area21090 Å2
MethodPISA
3
E: Pictet-Spenglerase
F: Pictet-Spenglerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9334
Polymers70,3572
Non-polymers5772
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-47 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.083, 94.083, 193.415
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
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
#2: Chemical
ChemComp-A1B1P / (1S,3S)-1-(2-carboxyethyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylic acid


Mass: 288.299 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H16N2O4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Sodium chloride, bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.38
ReflectionResolution: 2.87→47.04 Å / Num. obs: 43504 / % possible obs: 99.3 % / Redundancy: 5.1 % / CC1/2: 0.997 / Net I/σ(I): 7.5
Reflection shellResolution: 2.87→2.94 Å / Num. unique obs: 1891 / CC1/2: 0.538

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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: 2.87→47.04 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 41.46 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2613 2023 4.79 %
Rwork0.2238 --
obs0.2431 42258 96.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.87→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13241 0 126 0 13367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.551
X-RAY DIFFRACTIONf_dihedral_angle_d19.5764916
X-RAY DIFFRACTIONf_chiral_restr0.1042096
X-RAY DIFFRACTIONf_plane_restr0.0252409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-2.940.28651110.28042482X-RAY DIFFRACTION80
2.94-3.020.31261260.29372735X-RAY DIFFRACTION88
3.02-3.110.32731380.29382804X-RAY DIFFRACTION89
3.11-3.210.33241340.2812802X-RAY DIFFRACTION90
3.21-3.320.36031380.29482863X-RAY DIFFRACTION91
3.32-3.460.31151420.28762902X-RAY DIFFRACTION93
3.46-3.610.29231470.2642944X-RAY DIFFRACTION94
3.61-3.80.30311470.25942924X-RAY DIFFRACTION94
3.81-4.040.31781280.24722986X-RAY DIFFRACTION95
4.04-4.360.27131480.2292951X-RAY DIFFRACTION95
4.36-4.790.31991540.20782982X-RAY DIFFRACTION95
4.79-5.490.26551510.20872963X-RAY DIFFRACTION95
5.49-6.910.24411500.23532967X-RAY DIFFRACTION95
6.91-47.040.26451490.22052990X-RAY DIFFRACTION95

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