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

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Basic information

Entry
Database: PDB / ID: 9qvp
TitleCrystal structure of the CtaG_H128A variant from Ruminiclostridium cellulolyticum (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 / homologyButirosin biosynthesis protein H N-terminal domain-containing protein
Function and homology information
Biological speciesRuminiclostridium cellulolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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


Theoretical massNumber of molelcules
Total (without water)74,2502
Polymers74,2502
Non-polymers00
Water97354
1
A: Butirosin biosynthesis protein H N-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)37,1251
Polymers37,1251
Non-polymers00
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)37,1251
Polymers37,1251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.150, 100.140, 100.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, 25% PEG 3000

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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: 2.1→30 Å / Num. obs: 35280 / % possible obs: 97.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.2
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4535 / % possible all: 97.7

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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: 2.1→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.271 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 1763 5 %RANDOM
Rwork0.2024 ---
obs0.2041 33504 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.91 Å2 / Biso mean: 38.711 Å2 / Biso min: 24 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å2-0 Å2
2---2.88 Å2-0 Å2
3---2.27 Å2
Refinement stepCycle: final / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5108 0 0 54 5162
Biso mean---37.61 -
Num. residues----612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135226
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174623
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.6367046
X-RAY DIFFRACTIONr_angle_other_deg1.1081.57410783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1215610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62424.249313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09815949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4781520
X-RAY DIFFRACTIONr_chiral_restr0.0410.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021132
X-RAY DIFFRACTIONr_rigid_bond_restr0.38839849
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 130 -
Rwork0.268 2472 -
all-2602 -
obs--98.41 %
Refinement TLS params.

T22: 0.0312 Å2 / 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)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00180.0002-0.00120-0.00010.00120.0006-0.0011-0.0008-0-0.0009-0.00010.0008-0.00120.00030.0057-0.0006-0.00110.00040.000512.22433.482223.9408
20.0089-0.00260.00340.0124-0.00540.00310.001-0.0006-0.0003-0.00540.00040.00390.00220.002-0.00130.0028-0.0009-0.0014-0.00070.0015-16.71312.99532.4729
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 309
2X-RAY DIFFRACTION2B3 - 309

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