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- PDB-6x6v: Crystal structure of inactive enzymatic binary toxin component fr... -

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Basic information

Entry
Database: PDB / ID: 6x6v
TitleCrystal structure of inactive enzymatic binary toxin component from Clostridium difficile in complex with NADPH
ComponentsCdtA
KeywordsTOXIN / TRANSFERASE / RIBOSYLTRANSFERASE / CDTA
Function / homologyBinary exotoxin A, clostridial type / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / extracellular region / Chem-NDP / CdtA
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsPozharski, E.
CitationJournal: To Be Published
Title: Crystal structure of inactive enzymatic binary toxin component from Clostridium difficile in complex with NADPH
Authors: Pozharski, E.
History
DepositionMay 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CdtA
B: CdtA
C: CdtA
D: CdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,1298
Polymers198,1474
Non-polymers2,9824
Water11,476637
1
A: CdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2822
Polymers49,5371
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2822
Polymers49,5371
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2822
Polymers49,5371
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2822
Polymers49,5371
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.770, 101.100, 104.330
Angle α, β, γ (deg.)98.800, 112.360, 106.720
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CdtA


Mass: 49536.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: cdtA / Production host: Escherichia coli (E. coli) / References: UniProt: F5B5W8
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.73 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.2 M Sodium dihydrogen phosphate/0.8 M dipotassium hydrogen phosphate, 0.2 M Lithium sulfate, 0.1 M CAPS pH 10.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→38.91 Å / Num. obs: 114511 / % possible obs: 98.9 % / Redundancy: 1.97 % / CC1/2: 0.957 / Net I/σ(I): 2.85
Reflection shellResolution: 2.4→2.47 Å / Num. unique obs: 17202 / CC1/2: 0.34

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wn4

2wn4


Resolution: 2.42→38.91 Å / Cor.coef. Fo:Fc: 0.8861 / Cor.coef. Fo:Fc free: 0.8534 / SU R Cruickshank DPI: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.257 / SU Rfree Blow DPI: 0.202 / SU Rfree Cruickshank DPI: 0.207
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 5428 5.06 %RANDOM
Rwork0.2062 ---
obs0.2076 107350 98.4 %-
Displacement parametersBiso max: 117.59 Å2 / Biso mean: 31.68 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-3.166 Å2-1.9468 Å2-2.4487 Å2
2---2.0909 Å2-1.9649 Å2
3----1.0751 Å2
Refine analyzeLuzzati coordinate error obs: 0.385 Å
Refinement stepCycle: final / Resolution: 2.42→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13382 0 192 637 14211
Biso mean--45.11 26.81 -
Num. residues----1664
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4984SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes395HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2007HARMONIC5
X-RAY DIFFRACTIONt_it13905HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1833SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16551SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13905HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg18832HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion19.36
LS refinement shellResolution: 2.42→2.48 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2429 372 4.79 %
Rwork0.2156 7390 -
all0.2169 7762 -
obs--96.95 %
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)
11.6086-0.3655-0.28121.5606-0.13110.90480.0787-0.07530.0105-0.06020.0169-0.1512-0.02460.2442-0.0955-0.2115-0.02020.00760.04130.0008-0.02724.7623-8.0893-19.4449
22.3417-0.2795-0.27760.94890.0670.7133-0.0126-0.07050.11910.04190.04710.0704-0.08180.0896-0.0345-0.1558-0.04720.062-0.04250.0564-0.0821-2.17696.6416-14.1935
31.18250.3650.22130.8844-0.02880.9960.0948-0.02170.09660.0002-0.06190.13150.0766-0.0208-0.0328-0.2269-0.01460.0437-0.06330.02390.0246-20.676633.8168-52.6993
41.9117-0.06940.01540.5981-0.14940.99320.0836-0.29450.05870.0892-0.0745-0.0053-0.1023-0.051-0.0092-0.1861-0.0530.0477-0.12780.0339-0.00784.853736.2055-35.4621
51.65280.24540.35570.88320.29260.33570.08630.01950.00480.0792-0.0321-0.00230.0720.1511-0.0543-0.2256-0.01830.0285-0.01980.0264-0.022830.603323.2463-66.5515
62.61170.5260.59641.0226-0.23440.47250.06460.247-0.4571-0.1114-0.0199-0.05650.1084-0.0119-0.0447-0.17140.01810.02-0.0653-0.0134-0.03565.04617.1024-73.4872
71.6945-0.0528-0.69880.9517-0.33021.850.10450.1128-0.1497-0.0394-0.11680.2697-0.07-0.21180.0123-0.2787-0.01450.0175-0.0785-0.02940.0679-24.7943-20.6592-37.2227
82.3781-0.5483-0.60270.5987-0.26650.42580.04560.4317-0.0608-0.1613-0.0678-0.01060.0099-0.07240.0222-0.16030.0180.0094-0.11240.0105-0.00292.0924-21.4808-52.7942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|5 - 218}A5 - 218
2X-RAY DIFFRACTION2{A|219 - 420}A219 - 420
3X-RAY DIFFRACTION3{B|5 - 218}B5 - 218
4X-RAY DIFFRACTION4{B|219 - 420}B219 - 420
5X-RAY DIFFRACTION5{C|5 - 218}C5 - 218
6X-RAY DIFFRACTION6{C|219 - 420}C219 - 420
7X-RAY DIFFRACTION7{D|5 - 218}D5 - 218
8X-RAY DIFFRACTION8{D|219 - 420}D219 - 420

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