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- PDB-9qvr: Crystal structure of the CtaG_H128A variant from Ruminiclostridiu... -

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Basic information

Entry
Database: PDB / ID: 9qvr
TitleCrystal structure of the CtaG_H128A variant from Ruminiclostridium cellulolyticum in complex with PHBA (P2(1)2(1)2(1)-medium)
ComponentsButirosin biosynthesis protein H N-terminal domain-containing protein
KeywordsLIGASE / Amide Bond Formation / Antibiotics / Biosynthesis / Carrier proteins / Enzymes / Nonribosomal Peptide Synthetases
Function / homologyP-HYDROXYBENZALDEHYDE / Butirosin biosynthesis protein H N-terminal domain-containing protein
Function and homology information
Biological speciesRuminiclostridium cellulolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
B: Butirosin biosynthesis protein H N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5865
Polymers74,2502
Non-polymers3363
Water4,414245
1
A: Butirosin biosynthesis protein H N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3393
Polymers37,1251
Non-polymers2142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Butirosin biosynthesis protein H N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2472
Polymers37,1251
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.690, 99.670, 100.740
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: 37124.754 Da / Num. of mol.: 2 / Mutation: H128A
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-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Ammoniumphosphate, 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: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 65109 / % possible obs: 97.4 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 18
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 10372 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.535 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22936 3255 5 %RANDOM
Rwork0.20265 ---
obs0.20406 61844 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.743 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--1.15 Å2-0 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5126 0 6 245 5377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135251
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184639
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.6427079
X-RAY DIFFRACTIONr_angle_other_deg1.2271.5810815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12624.249313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83215947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5161520
X-RAY DIFFRACTIONr_chiral_restr0.0560.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025884
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021140
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_it1.1322.042446
X-RAY DIFFRACTIONr_mcbond_other1.1322.0392445
X-RAY DIFFRACTIONr_mcangle_it1.5373.0623054
X-RAY DIFFRACTIONr_mcangle_other1.5373.0633055
X-RAY DIFFRACTIONr_scbond_it1.2182.3572805
X-RAY DIFFRACTIONr_scbond_other1.2182.3572806
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6363.4284026
X-RAY DIFFRACTIONr_long_range_B_refined2.38423.8916060
X-RAY DIFFRACTIONr_long_range_B_other2.32423.7726013
X-RAY DIFFRACTIONr_rigid_bond_restr0.52339890
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 242 -
Rwork0.305 4597 -
obs--99.53 %

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