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- PDB-9lmn: Crystal structure of a polyketide ABM/SchA-like domain-containing... -

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Basic information

Entry
Database: PDB / ID: 9lmn
TitleCrystal structure of a polyketide ABM/SchA-like domain-containing protein WhiE-ORFI from Streptomyces coelicolor
Components42.8 kDa protein in whiE locus
KeywordsANTIBIOTIC / Decarboxylase / polyketide biosynthesis
Function / homologySchA/CurD-like domain / SchA/CurD like domain / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Dimeric alpha-beta barrel / 42.8 kDa protein in whiE locus
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJiang, K. / Qu, X.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32425033 China
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Terminal Carboxyl Editing Drives Divergence in Fasamycin and Anthrabenzoxocinone Biosynthesis.
Authors: Jiang, K. / Zhu, C. / Gao, Y. / Dai, Y. / Yan, X. / Yang, L. / Jiang, M. / Lin, Z. / Deng, Z. / Luo, S. / Qu, X.
History
DepositionJan 19, 2025Deposition site: PDBJ / Processing site: PDBC
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
A: 42.8 kDa protein in whiE locus
B: 42.8 kDa protein in whiE locus


Theoretical massNumber of molelcules
Total (without water)85,7942
Polymers85,7942
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-19 kcal/mol
Surface area29870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.820, 75.850, 142.010
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 42.8 kDa protein in whiE locus / WhiE ORF I


Mass: 42896.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO5320, SC6G9.13
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P23158
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M Magnesium chloride hexahydrate, 0.1 M Sodium acetate trihydrate, 0.1 M Bis-Tris, 15% v/v PEG Smear Broad at pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→40.158 Å / Num. obs: 36966 / % possible obs: 99.7 % / Redundancy: 12.7 % / Biso Wilson estimate: 43.47 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.36 Å / Num. unique obs: 2628 / CC1/2: 0.673

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→36.63 Å / SU ML: 0.309 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2728 1828 4.95 %
Rwork0.238 35069 -
obs0.2397 36897 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5464 0 0 176 5640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01265570
X-RAY DIFFRACTIONf_angle_d1.84017601
X-RAY DIFFRACTIONf_chiral_restr0.0892869
X-RAY DIFFRACTIONf_plane_restr0.03671032
X-RAY DIFFRACTIONf_dihedral_angle_d26.21732041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.36421380.30282596X-RAY DIFFRACTION98.91
2.36-2.430.30271270.29572649X-RAY DIFFRACTION99.21
2.43-2.510.31461790.28392631X-RAY DIFFRACTION99.19
2.51-2.60.33241120.27682676X-RAY DIFFRACTION99.25
2.6-2.70.31711270.28262688X-RAY DIFFRACTION99.4
2.7-2.830.34971450.27822684X-RAY DIFFRACTION99.72
2.83-2.980.32331370.28272664X-RAY DIFFRACTION99.64
2.98-3.160.30821450.27612720X-RAY DIFFRACTION99.79
3.16-3.410.30031440.25632657X-RAY DIFFRACTION99.68
3.41-3.750.2591190.22592751X-RAY DIFFRACTION99.86
3.75-4.290.24441480.21662721X-RAY DIFFRACTION99.86
4.29-5.40.23791460.19662776X-RAY DIFFRACTION99.93
5.4-36.630.22831610.21052856X-RAY DIFFRACTION99.18

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