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

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Basic information

Entry
Database: PDB / ID: 9qvj
TitleCrystal structure of CtaG from Ruminiclostridium cellulolyticum (P2(1)-medium)
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: 1.55 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)74,6823
Polymers74,5902
Non-polymers921
Water3,171176
1
A: Butirosin biosynthesis protein H N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3872
Polymers37,2951
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Butirosin biosynthesis protein H N-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)37,2951
Polymers37,2951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.070, 60.350, 82.960
Angle α, β, γ (deg.)90.000, 99.040, 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: 37294.965 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES, 0.2M LiCl, 0.05 M Mg2SO4, 8% PEG 8000

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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: Mar 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 81961 / % possible obs: 97.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 16.9
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 14022 / % possible all: 98.6

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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: 1.55→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.834 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1874 4097 5 %RANDOM
Rwork0.1573 ---
obs0.1589 77855 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.32 Å2 / Biso mean: 27.434 Å2 / Biso min: 13.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å2-0.62 Å2
2---2.22 Å20 Å2
3---1.34 Å2
Refinement stepCycle: final / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5134 0 6 176 5316
Biso mean--43.52 36.3 -
Num. residues----614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135273
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174655
X-RAY DIFFRACTIONr_angle_refined_deg1.241.6357111
X-RAY DIFFRACTIONr_angle_other_deg1.3591.57410859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67324.227317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03115955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.941520
X-RAY DIFFRACTIONr_chiral_restr0.0660.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025907
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021145
X-RAY DIFFRACTIONr_rigid_bond_restr1.68639928
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 303 -
Rwork0.282 5769 -
all-6072 -
obs--98.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0091-0.00390.00370.0031-0.00460.008-0.00030.00060.00050.0005-0.0001-0.0003-0.00110.0010.00040.0091-0.00030.00310.0148-0.00090.0012-3.8143-14.250831.2673
20.00380.002-0.0080.0164-0.01490.0243-0.0005-0.0022-0.00070.00190.00080.0024-0.00070.003-0.00040.00830.00040.00280.0153-0.00060.0015-25.145-13.876-9.3773
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 309
2X-RAY DIFFRACTION2B3 - 309

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