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- PDB-8aif: TapA acts as specific chaperone in TasA non-amyloid filament formation -

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Basic information

Entry
Database: PDB / ID: 8aif
TitleTapA acts as specific chaperone in TasA non-amyloid filament formation
ComponentsYqxM protein required for localization of TasA to extracellular matrix
KeywordsSTRUCTURAL PROTEIN / Bacillus subtilis / Biofilm / TasA / TapA/YqxM
Function / homologybacterial biofilm matrix / TasA anchoring/assembly protein / Signal peptide, camelysin / NITRATE ION / YqxM protein required for localization of TasA to extracellular matrix
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.07 Å
AuthorsRoske, Y. / Heinemann, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: TapA acts as specific chaperone in TasA filament formation by strand complementation.
Authors: Roske, Y. / Lindemann, F. / Diehl, A. / Cremer, N. / Higman, V.A. / Schlegel, B. / Leidert, M. / Driller, K. / Turgay, K. / Schmieder, P. / Heinemann, U. / Oschkinat, H.
History
DepositionJul 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YqxM protein required for localization of TasA to extracellular matrix
B: YqxM protein required for localization of TasA to extracellular matrix
C: YqxM protein required for localization of TasA to extracellular matrix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,77310
Polymers41,3393
Non-polymers4347
Water13,385743
1
A: YqxM protein required for localization of TasA to extracellular matrix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8422
Polymers13,7801
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YqxM protein required for localization of TasA to extracellular matrix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0285
Polymers13,7801
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: YqxM protein required for localization of TasA to extracellular matrix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9043
Polymers13,7801
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.199, 52.936, 167.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A72 - 189
2114C72 - 189

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.204959, -0.951521, -0.229345), (-0.953645, -0.246889, 0.172067), (-0.220348, 0.183447, -0.958016)13.36309, 22.0506, -23.886869

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Components

#1: Protein YqxM protein required for localization of TasA to extracellular matrix


Mass: 13779.772 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_0967 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164X7F2
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 24% PEG3350, 0.35M LiNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.07→38.44 Å / Num. obs: 153127 / % possible obs: 98.8 % / Redundancy: 3.53 % / CC1/2: 0.999 / Rrim(I) all: 0.066 / Net I/σ(I): 9.77
Reflection shellResolution: 1.07→1.13 Å / Num. unique obs: 24261 / CC1/2: 0.3 / Rrim(I) all: 0.154

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HQC

6hqc


Resolution: 1.07→38.44 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.003 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1766 2100 1.4 %RANDOM
Rwork0.1482 ---
obs0.1486 151026 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.49 Å2 / Biso mean: 18.961 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2--1.94 Å2-0 Å2
3----2.97 Å2
Refinement stepCycle: final / Resolution: 1.07→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 28 743 3630
Biso mean--35.7 38.02 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133067
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162945
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.654149
X-RAY DIFFRACTIONr_angle_other_deg1.421.5986887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0115392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.90623.971136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13715598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.163159
X-RAY DIFFRACTIONr_chiral_restr0.0830.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02662
X-RAY DIFFRACTIONr_rigid_bond_restr4.46736012
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1735 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.950.5
MEDIUM THERMAL7.072
LS refinement shellResolution: 1.07→1.097 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 151 -
Rwork0.372 10833 -
all-10984 -
obs--96.72 %
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)
10.0039-0.00440.00710.03020.00250.0202-0.00050.00080.00150.00020.00070.00040.00350.0023-0.00030.0089-0.0001-0.00060.0004-0.00130.03138.578-3.0798-6.309
20.0099-0.00390.01180.0058-0.01060.02340.0009-0-0.00080.0010.0015-0.0009-0.0001-0.0029-0.00240.00680.00020.00060.002-0.00160.03147.2988-13.2472-38.064
30.0019-0.0002-0.00250.0399-0.00940.0080.0007-0.00030.00220.0028-0.0041-0.0007-0.00010.00180.00340.007-0.00030.00020.001-0.00160.033818.967614.3498-19.9219
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A72 - 301
2X-RAY DIFFRACTION2B71 - 201
3X-RAY DIFFRACTION3C71 - 188

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