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- PDB-9qvs: Crystal structure of the CtaG_D144N variant from Ruminiclostridiu... -

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Basic information

Entry
Database: PDB / ID: 9qvs
TitleCrystal structure of the CtaG_D144N variant from Ruminiclostridium cellulolyticum (P2(1)-small)
ComponentsButirosin biosynthesis protein H N-terminal domain-containing protein
KeywordsLIGASE / Amide Bond Formation / Antibiotics / Biosynthesis / Carrier proteins / Enzymes / Nonribosomal Peptide Synthetases
Function / homologyButirosin biosynthesis protein H N-terminal domain-containing protein
Function and homology information
Biological speciesRuminiclostridium cellulolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsGude, F. / Bohne, A. / Dell, M. / Franke, J. / Dunbar, K.L. / Groll, M. / Hertweck, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Chem / Year: 2025
Title: Distal peptide elongation by a protease-like ligase and two distinct carrier proteins
Authors: Gude, F. / Bohne, A. / Dell, M. / Franke, J. / Dunbar, K.L. / Groll, M. / Hertweck, C.
History
DepositionApr 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Butirosin biosynthesis protein H N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2142
Polymers37,1911
Non-polymers231
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.610, 60.280, 54.840
Angle α, β, γ (deg.)90.000, 108.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Butirosin biosynthesis protein H N-terminal domain-containing protein


Mass: 37190.840 Da / Num. of mol.: 1 / Mutation: D144N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium cellulolyticum (bacteria)
Gene: Ccel_3254 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8I0Y7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.96 Å3/Da / Density % sol: 37.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Potassiumphosphate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 49807 / % possible obs: 97.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.3
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 8941 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XFITdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.937 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1825 2490 5 %RANDOM
Rwork0.1561 ---
obs0.1574 47311 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.6 Å2 / Biso mean: 28.436 Å2 / Biso min: 13.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.1 Å2
2---0.8 Å2-0 Å2
3---0.83 Å2
Refinement stepCycle: final / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 1 119 2695
Biso mean--32.53 33.5 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132635
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172331
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.6353553
X-RAY DIFFRACTIONr_angle_other_deg1.411.5745437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4115307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88924.241158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24915479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1411510
X-RAY DIFFRACTIONr_chiral_restr0.0710.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022952
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02570
X-RAY DIFFRACTIONr_rigid_bond_restr1.92334966
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 179 -
Rwork0.314 3397 -
all-3576 -
obs--95.54 %

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