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- PDB-9qvk: Crystal structure of the CtaG_C11A variant from Ruminiclostridium... -

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Basic information

Entry
Database: PDB / ID: 9qvk
TitleCrystal structure of the CtaG_C11A 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: 1.75 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


Theoretical massNumber of molelcules
Total (without water)37,1601
Polymers37,1601
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.660, 60.280, 54.660
Angle α, β, γ (deg.)90.00, 108.84, 90.00
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: 37159.762 Da / Num. of mol.: 1 / Mutation: C11A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.96 Å3/Da / Density % sol: 37.17 %
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: Jul 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 27764 / % possible obs: 95.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 14.1
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4323 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 9.517 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21803 1388 5 %RANDOM
Rwork0.1838 ---
obs0.18553 26370 95.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.615 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å2-0 Å25.34 Å2
2---4.78 Å20 Å2
3----0.46 Å2
Refinement stepCycle: 1 / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 0 33 2599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132626
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172321
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.6353541
X-RAY DIFFRACTIONr_angle_other_deg1.2291.5745413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64924.241158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10515476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1551510
X-RAY DIFFRACTIONr_chiral_restr0.0610.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02569
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5554.2431227
X-RAY DIFFRACTIONr_mcbond_other2.554.2411226
X-RAY DIFFRACTIONr_mcangle_it3.1826.3741532
X-RAY DIFFRACTIONr_mcangle_other3.1856.3761533
X-RAY DIFFRACTIONr_scbond_it2.9134.6711399
X-RAY DIFFRACTIONr_scbond_other2.9024.6711399
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6816.852009
X-RAY DIFFRACTIONr_long_range_B_refined4.01348.0752926
X-RAY DIFFRACTIONr_long_range_B_other4.01548.0852925
X-RAY DIFFRACTIONr_rigid_bond_restr0.88834947
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 105 -
Rwork0.307 1982 -
obs--96.84 %
Refinement TLS params.Method: refined / Origin x: 2.1135 Å / Origin y: 13.1503 Å / Origin z: -17.9978 Å
111213212223313233
T0.0241 Å2-0.0009 Å2-0.0204 Å2-0.023 Å20.0014 Å2--0.0173 Å2
L0.0565 °20.0175 °20.0036 °2-0.0836 °20.0384 °2--0.1523 °2
S0.003 Å °0.0011 Å °-0.0023 Å °0.003 Å °-0.0046 Å °-0.0054 Å °-0.0004 Å °-0.0122 Å °0.0016 Å °

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