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- PDB-6u8t: Crystal structure of YopT domain of Pasteurella Multocida PfhB2-toxin -

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Basic information

Entry
Database: PDB / ID: 6u8t
TitleCrystal structure of YopT domain of Pasteurella Multocida PfhB2-toxin
ComponentsPfhB2
KeywordsHYDROLASE / Cysteine Protease
Function / homology
Function and homology information


AMPylase activity / cysteine-type endopeptidase activity / extracellular region / membrane
Similarity search - Function
Peptidase C58, Yersinia/Haemophilus virulence surface antigen / Yersinia/Haemophilus virulence surface antigen / Fido domain-containing protein / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Peptidase C58, YopT-type domain / Fido-like domain superfamily ...Peptidase C58, Yersinia/Haemophilus virulence surface antigen / Yersinia/Haemophilus virulence surface antigen / Fido domain-containing protein / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Peptidase C58, YopT-type domain / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Pectin lyase fold / Pectin lyase fold/virulence factor / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / PfhB2
Similarity search - Component
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å
AuthorsKumar, S. / Mattoo, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM10092 United States
CitationJournal: To Be Published
Title: Crystal structure of YopT domain of Pasteurella Multocida PfhB2-Toxin
Authors: Kumar, S. / Mattoo, S.
History
DepositionSep 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PfhB2
C: PfhB2
B: PfhB2
D: PfhB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5918
Polymers99,2964
Non-polymers2944
Water4,342241
1
A: PfhB2
B: PfhB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9426
Polymers49,6482
Non-polymers2944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PfhB2
D: PfhB2


Theoretical massNumber of molelcules
Total (without water)49,6482
Polymers49,6482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.652, 62.957, 164.342
Angle α, β, γ (deg.)90.00, 93.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.621173, 0.60352, 0.499908), (-0.047759, 0.607564, -0.792833), (-0.782217, -0.516362, -0.348579)-18.70944, 16.56071, 68.29498

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Components

#1: Protein
PfhB2


Mass: 24824.078 Da / Num. of mol.: 4 / Mutation: C3733S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida (strain Pm70) (bacteria)
Strain: Pm70 / Gene: pfhB2, PM0059 / Plasmid: pSMT3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9CPH9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.27 % / Description: Rod Shape
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Magnesium Acetate and PEG 3350 22%

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Data collection

DiffractionMean temperature: 80.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9762 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2017
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.39→30 Å / Num. obs: 37166 / % possible obs: 96.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 51.9 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.088 / Net I/σ(I): 16.9
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3306 / CC1/2: 0.79 / Rrim(I) all: 0.587 / % possible all: 86.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data reduction
HKL-2000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.39→29.41 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 17.717 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.64 / ESU R Free: 0.288 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24467 1650 4.9 %RANDOM
Rwork0.19928 ---
obs0.20156 31955 88.34 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 51.211 Å2
Baniso -1Baniso -2Baniso -3
1--3.08 Å2-0 Å2-1.71 Å2
2--1.32 Å2-0 Å2
3---1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.39→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6654 0 19 241 6914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136805
X-RAY DIFFRACTIONr_bond_other_d0.0010.0186196
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.6379132
X-RAY DIFFRACTIONr_angle_other_deg1.2731.58614471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1655846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33824.922319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.738151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9861512
X-RAY DIFFRACTIONr_chiral_restr0.1390.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027582
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021378
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 73 -
Rwork0.267 1337 -
obs--49.63 %
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)
10.56140.1379-0.54091.8197-1.01672.21860.0820.27610.107-0.58130.06740.0024-0.1941-0.3843-0.14940.43110.06650.11220.15050.03850.13113.43410.65256.76
22.44561.8324-1.32873.6982-1.29471.5189-0.09-0.1527-0.1749-0.0228-0.1507-0.50130.06140.23970.24060.56980.07730.10610.27830.01450.1703-4.00516.1518.593
30.7571-0.46580.08692.2027-0.54322.23040.09370.06190.1107-0.1122-0.0597-0.3769-0.39160.0039-0.03390.2161-0.00380.12490.0093-0.00390.15139.36311.19570.518
42.010.9542-1.22181.5639-0.66031.5931-0.13540.22030.1839-0.06690.1910.24240.0343-0.2613-0.05560.65560.06660.1550.220.01120.171-17.98915.64718.14
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3696 - 3916
2X-RAY DIFFRACTION2C3696 - 3916
3X-RAY DIFFRACTION3B3696 - 3916
4X-RAY DIFFRACTION4D3697 - 3917

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