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- PDB-9quz: Crystal structure of CtaG from Ruminiclostridium cellulolyticum (... -

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Basic information

Entry
Database: PDB / ID: 9quz
TitleCrystal structure of CtaG 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: 1.4 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)37,3483
Polymers37,1921
Non-polymers1562
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-9 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.760, 60.300, 54.910
Angle α, β, γ (deg.)90.000, 108.910, 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: 37191.824 Da / Num. of mol.: 1
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.: 143 / 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: 1.97 Å3/Da / Density % sol: 37.54 %
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: May 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 55440 / % possible obs: 97.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 14.4
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 10309 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.147 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1891 2771 5 %RANDOM
Rwork0.1568 ---
obs0.1584 52663 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.35 Å2 / Biso mean: 27.645 Å2 / Biso min: 15.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å21.07 Å2
2---3 Å2-0 Å2
3---1.63 Å2
Refinement stepCycle: final / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 9 143 2727
Biso mean--50.47 36.91 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132642
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172331
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.6353562
X-RAY DIFFRACTIONr_angle_other_deg1.3651.5745437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0165307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41624.241158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65215479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1311510
X-RAY DIFFRACTIONr_chiral_restr0.0630.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
X-RAY DIFFRACTIONr_rigid_bond_restr1.20434973
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 206 -
Rwork0.36 3919 -
all-4125 -
obs--98.1 %
Refinement TLS params.Method: refined / Origin x: 2.1195 Å / Origin y: 13.2151 Å / Origin z: -18.0713 Å
111213212223313233
T0.004 Å20.0005 Å20.003 Å2-0.013 Å2-0.0001 Å2--0.0022 Å2
L0.006 °20.0018 °2-0.0062 °2-0.0006 °2-0.0019 °2--0.0065 °2
S0.0003 Å °0.0014 Å °0.0008 Å °0.0002 Å °0.0004 Å °0.0003 Å °-0.0002 Å °-0.002 Å °-0.0007 Å °

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