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- PDB-5v1u: TbiB1 in Complex with the TbiA(beta) Leader Peptide -

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Basic information

Entry
Database: PDB / ID: 5v1u
TitleTbiB1 in Complex with the TbiA(beta) Leader Peptide
Components
  • TbiA(beta) Thr(-5)Glu Leader
  • TbiB1
KeywordsPROTEIN BINDING / Lasso Peptide / RiPP / Peptide Binding
Function / homologyCoenzyme PQQ synthesis protein D / Coenzyme PQQ synthesis protein D superfamily / Coenzyme PQQ synthesis protein D (PqqD) / Uncharacterized protein / PqqD family protein
Function and homology information
Biological speciesThermobaculum terrenum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.052 Å
AuthorsChekan, J.R. / Nair, S.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Steric complementarity directs sequence promiscuous leader binding in RiPP biosynthesis.
Authors: Chekan, J.R. / Ongpipattanakul, C. / Nair, S.K.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TbiB1
B: TbiB1
C: TbiB1
D: TbiB1
E: TbiA(beta) Thr(-5)Glu Leader
F: TbiA(beta) Thr(-5)Glu Leader
G: TbiA(beta) Thr(-5)Glu Leader
H: TbiA(beta) Thr(-5)Glu Leader
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,23519
Polymers49,5168
Non-polymers71911
Water3,837213
1
A: TbiB1
E: TbiA(beta) Thr(-5)Glu Leader
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5104
Polymers12,3792
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-12 kcal/mol
Surface area5830 Å2
MethodPISA
2
B: TbiB1
F: TbiA(beta) Thr(-5)Glu Leader
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7067
Polymers12,3792
Non-polymers3275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-11 kcal/mol
Surface area6050 Å2
MethodPISA
3
C: TbiB1
G: TbiA(beta) Thr(-5)Glu Leader
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5755
Polymers12,3792
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-13 kcal/mol
Surface area6000 Å2
MethodPISA
4
D: TbiB1
H: TbiA(beta) Thr(-5)Glu Leader
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4443
Polymers12,3792
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-14 kcal/mol
Surface area6250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.155, 48.630, 55.287
Angle α, β, γ (deg.)78.30, 66.88, 88.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
TbiB1


Mass: 10132.303 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobaculum terrenum (strain ATCC BAA-798 / YNP1) (bacteria)
Strain: ATCC BAA-798 / YNP1 / Gene: Tter_2832 / Production host: Escherichia coli (E. coli) / References: UniProt: D1CIZ5
#2: Protein/peptide
TbiA(beta) Thr(-5)Glu Leader


Mass: 2246.579 Da / Num. of mol.: 4 / Fragment: UNP residues 1-20 / Source method: obtained synthetically / Source: (synth.) Thermobaculum terrenum (bacteria) / References: UniProt: D1CIY7
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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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: 41.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4% isopropanol, 0.05 M zinc acetate, 0.1 M sodium cacodylate (pH 6.5), 6 mg/mL Protein, 1 mM TbiA(beta) T(-5)E

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 23055 / % possible obs: 91.2 % / Redundancy: 2.7 % / Rsym value: 0.041 / Net I/σ(I): 17.6
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1003 / Rsym value: 0.242 / % possible all: 82.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.052→31.257 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.23
RfactorNum. reflection% reflection
Rfree0.2399 1055 4.8 %
Rwork0.2005 --
obs0.2025 21979 86.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.052→31.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 11 213 3403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043244
X-RAY DIFFRACTIONf_angle_d0.8534402
X-RAY DIFFRACTIONf_dihedral_angle_d10.7681201
X-RAY DIFFRACTIONf_chiral_restr0.038517
X-RAY DIFFRACTIONf_plane_restr0.005563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0519-2.14530.2631930.21782069X-RAY DIFFRACTION69
2.1453-2.25840.33571060.26362103X-RAY DIFFRACTION70
2.2584-2.39980.30061410.23782504X-RAY DIFFRACTION84
2.3998-2.5850.2771330.22782939X-RAY DIFFRACTION98
2.585-2.8450.27741520.21942986X-RAY DIFFRACTION98
2.845-3.25630.2611460.21062960X-RAY DIFFRACTION98
3.2563-4.10110.23051110.18132433X-RAY DIFFRACTION81
4.1011-31.26030.18091730.16822930X-RAY DIFFRACTION98

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