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

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Basic information

Entry
Database: PDB / ID: 9qvl
TitleCrystal structure of the CtaG_C11A variant from Ruminiclostridium cellulolyticum (P2(1)2(1)2(1)-small)
ComponentsButirosin biosynthesis protein H N-terminal domain-containing protein
KeywordsLIGASE / Amide Bond Formation / Antibiotics / Biosynthesis / Carrier proteins / Enzymes / Nonribosomal Peptide Synthetases
Function / homologyIMIDAZOLE / NICKEL (II) ION / Butirosin biosynthesis protein H N-terminal domain-containing protein
Function and homology information
Biological speciesRuminiclostridium cellulolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)37,4685
Polymers37,1601
Non-polymers3094
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-10 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.770, 63.620, 83.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Sodiumphosphate, 20% PEG 3350

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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: 1.5→30 Å / Num. obs: 50719 / % possible obs: 96.1 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.8
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8790 / % possible all: 95.9

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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: 1.5→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.278 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20598 2534 5 %RANDOM
Rwork0.18466 ---
obs0.18585 48146 96.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.185 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å2-0 Å2
2---0.95 Å20 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 15 159 2776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132674
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172367
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.6333602
X-RAY DIFFRACTIONr_angle_other_deg1.1981.5755517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89624.214159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54415483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9171510
X-RAY DIFFRACTIONr_chiral_restr0.0470.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022993
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02581
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_it1.3022.6131248
X-RAY DIFFRACTIONr_mcbond_other1.3022.6091246
X-RAY DIFFRACTIONr_mcangle_it1.8323.9211557
X-RAY DIFFRACTIONr_mcangle_other1.8323.9231558
X-RAY DIFFRACTIONr_scbond_it1.512.9391426
X-RAY DIFFRACTIONr_scbond_other1.5092.941427
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.994.2962046
X-RAY DIFFRACTIONr_long_range_B_refined2.91930.9583095
X-RAY DIFFRACTIONr_long_range_B_other2.84330.7533063
X-RAY DIFFRACTIONr_rigid_bond_restr0.53635041
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 184 -
Rwork0.355 3482 -
obs--95.72 %

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