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- PDB-9nsc: Bacterial Pictet-Spenglerase KslB in complex with L-Trp -

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Basic information

Entry
Database: PDB / ID: 9nsc
TitleBacterial Pictet-Spenglerase KslB in complex with L-Trp
ComponentsPictet-Spenglerase
KeywordsBIOSYNTHETIC PROTEIN / Pictet-Spenglerase
Function / homologyCucumopine synthase, C-terminal helical bundle domain / Cucumopine synthase C-terminal helical bundle domain / TRYPTOPHAN / Cucumopine synthase C-terminal helical bundle domain-containing protein
Function and homology information
Biological speciesKitasatospora setae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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

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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)212,29612
Polymers211,0706
Non-polymers1,2256
Water00
1
A: Pictet-Spenglerase
B: Pictet-Spenglerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7654
Polymers70,3572
Non-polymers4082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-46 kcal/mol
Surface area21450 Å2
MethodPISA
2
C: Pictet-Spenglerase
D: Pictet-Spenglerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7654
Polymers70,3572
Non-polymers4082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-46 kcal/mol
Surface area21950 Å2
MethodPISA
3
E: Pictet-Spenglerase
F: Pictet-Spenglerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7654
Polymers70,3572
Non-polymers4082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-46 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.532, 94.532, 193.101
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 BL21(DE3) (bacteria) / References: UniProt: E4NIM4
#2: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H12N2O2 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 3350, Sodium Chloride, Bis-Tris / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 22, 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: 0.48
ReflectionResolution: 3.1→47.27 Å / Num. obs: 35035 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.924 / Net I/σ(I): 3.5
Reflection shellResolution: 3.1→3.15 Å / Num. unique obs: 1804 / CC1/2: 0.5

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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: 3.1→47.27 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.6002
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2342 2060 6 %
Rwork0.1765 32268 -
obs0.1899 34328 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.21 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13934 0 90 0 14024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01214392
X-RAY DIFFRACTIONf_angle_d1.463319696
X-RAY DIFFRACTIONf_chiral_restr0.09972226
X-RAY DIFFRACTIONf_plane_restr0.01772532
X-RAY DIFFRACTIONf_dihedral_angle_d17.64835177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.32651350.22222253X-RAY DIFFRACTION89.19
3.18-3.260.28211430.21252278X-RAY DIFFRACTION89.72
3.26-3.360.29851400.21532255X-RAY DIFFRACTION90.67
3.36-3.470.26291490.20412281X-RAY DIFFRACTION90.84
3.47-3.590.23141390.19532285X-RAY DIFFRACTION92.06
3.59-3.740.27981360.18852317X-RAY DIFFRACTION93.13
3.74-3.910.25871470.18322327X-RAY DIFFRACTION92.56
3.91-4.110.2221530.17992321X-RAY DIFFRACTION92.88
4.11-4.370.22371450.17362315X-RAY DIFFRACTION93.38
4.37-4.710.18171440.16222364X-RAY DIFFRACTION93.51
4.71-5.180.20771380.15992334X-RAY DIFFRACTION93.73
5.18-5.930.24581420.18632331X-RAY DIFFRACTION93.09
5.93-7.460.24181540.18562309X-RAY DIFFRACTION92.81
7.47-47.270.2421520.19852341X-RAY DIFFRACTION93.64

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