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

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Basic information

Entry
Database: PDB / ID: 9qvo
TitleCrystal structure of the CtaG_H128A 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 / homologyCARBONATE 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: 1.9 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)37,2813
Polymers37,1251
Non-polymers1562
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-8 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.780, 60.740, 54.960
Angle α, β, γ (deg.)90.000, 108.620, 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: 37124.754 Da / Num. of mol.: 1 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Potassiumphosphate, 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: Oct 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 22688 / % possible obs: 98 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3108 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 11.441 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1134 5 %RANDOM
Rwork0.1817 ---
obs0.1839 21547 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.63 Å2 / Biso mean: 43.291 Å2 / Biso min: 29.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0 Å23.96 Å2
2---1.05 Å2-0 Å2
3----1.83 Å2
Refinement stepCycle: final / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 9 47 2618
Biso mean--78.48 46.88 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132628
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172319
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.6353543
X-RAY DIFFRACTIONr_angle_other_deg1.1091.5745409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9185306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91624.268157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96415476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4641510
X-RAY DIFFRACTIONr_chiral_restr0.0410.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022943
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02567
X-RAY DIFFRACTIONr_rigid_bond_restr0.34434947
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 80 -
Rwork0.276 1521 -
all-1601 -
obs--94.18 %
Refinement TLS params.Method: refined / Origin x: 2.0234 Å / Origin y: 13.2262 Å / Origin z: -18.0963 Å
111213212223313233
T0.0178 Å2-0.0019 Å2-0.0227 Å2-0.0004 Å20.0031 Å2--0.0315 Å2
L0.0065 °2-0.0111 °2-0.0086 °2-0.0191 °20.0149 °2--0.0116 °2
S0.0033 Å °0.0007 Å °-0.0007 Å °-0.0043 Å °-0.0017 Å °-0.0013 Å °-0.0032 Å °-0.0011 Å °-0.0015 Å °

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