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- PDB-8qb1: C-terminal domain of mirolase from Tannerella forsythia -

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Basic information

Entry
Database: PDB / ID: 8qb1
TitleC-terminal domain of mirolase from Tannerella forsythia
ComponentsMirolase
KeywordsPROTEIN TRANSPORT / Type-IX Secretion System C-terminal secretion-signal domain
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
PKD-like domain / PKD-like domain / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily ...PKD-like domain / PKD-like domain / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Mirolase
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.601 Å
AuthorsGomis-Ruth, F.X. / Rodriguez-Banqueri, A. / Mizgalska, D. / Veillard, F. / Goulas, T. / Eckhard, U. / Potempa, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Open Biology / Year: 2024
Title: Structural and functional insights into the C-terminal signal domain of the Bacteroidetes type-IX secretion system.
Authors: Mizgalska, D. / Rodriguez-Banqueri, A. / Veillard, F. / Ksiazek, M. / Goulas, T. / Guevara, T. / Eckhard, U. / Potempa, J. / Gomis-Ruth, F.X.
History
DepositionAug 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mirolase
B: Mirolase
C: Mirolase
D: Mirolase
E: Mirolase
F: Mirolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,50120
Polymers59,5736
Non-polymers92814
Water8,575476
1
A: Mirolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0703
Polymers9,9291
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mirolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1104
Polymers9,9291
Non-polymers1813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mirolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0703
Polymers9,9291
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mirolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0703
Polymers9,9291
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Mirolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1104
Polymers9,9291
Non-polymers1813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Mirolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0703
Polymers9,9291
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.445, 81.445, 66.553
Angle α, β, γ (deg.)90, 90, 120
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Mirolase


Mass: 9928.908 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A7KVG3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein at 19 mg per mL in 5mM Tris-HCl pH 8.0 and 30% polyethylene glycol (PEG) 2000, 0.1 M potassium thiocyanide as reservoir solution.

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: h,-h-k,-l / Fraction: 0.423
ReflectionResolution: 1.6→48.41 Å / Num. obs: 65076 / % possible obs: 99.8 % / Redundancy: 11.2 % / Biso Wilson estimate: 23.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.127 / Net I/σ(I): 9
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 11.1 / Num. unique obs: 10842 / CC1/2: 0.943 / Rrim(I) all: 0.999 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.601→48.41 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.142 / SU Rfree Blow DPI: 0.13 / SU Rfree Cruickshank DPI: 0.129
RfactorNum. reflection% reflectionSelection details
Rfree0.3016 656 -RANDOM
Rwork0.2746 ---
obs0.2748 64887 99.7 %-
Displacement parametersBiso mean: 21.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.7542 Å20 Å20 Å2
2--0.7542 Å20 Å2
3----1.5084 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 1.601→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 50 476 4574
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084205HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.975694HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1502SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes692HARMONIC5
X-RAY DIFFRACTIONt_it4205HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion573SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies9HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact3758SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion14.75
LS refinement shellResolution: 1.601→1.62 Å
RfactorNum. reflection% reflection
Rfree0.3048 34 -
Rwork0.2399 --
obs--95.65 %
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)
12.1382-0.63620.54860.5769-0.23591.4918-0.02810.0396-0.0040.0396-0.0167-0.043-0.004-0.0430.0448-0.05660.00030.0094-0.0766-0.0139-0.077826.471321.1348-29.9541
2-0.00640.46310.01482.5475-0.6491.31610.02430.0808-0.07870.0808-0.09160.0461-0.07870.04610.0674-0.0510.0056-0.0053-0.0046-0.00940.03079.206511.198-38.4031
31.8379-1.6910.31860.5218-0.02480.6132-0.10090.004-0.01990.0040.04270.0335-0.01990.03350.0582-0.012-0.013-0.012-0.02780.00580.04425.552633.9784-17.8784
41.82290.4509-0.28630.7175-0.12741.3818-0.0084-0.03290.0175-0.0329-0.0249-0.07380.0175-0.07380.0333-0.06-0.0012-0.008-0.0712-0.0188-0.077126.469725.87345.1625
50.3365-0.4273-0.12432.4486-0.52681.54750.0056-0.05530.0535-0.0553-0.08490.08410.05350.08410.0793-0.0525-0.00890.0101-0.01420.00250.01969.189935.779613.6348
62.14411.4789-0.27890.993-0.09250.8973-0.08380.0120.0020.0120.01710.0070.0020.0070.0667-0.01240.01510.0095-0.03060.00510.00775.501512.9911-6.8938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|-2 - A|-1 A|706 - A|791 A|801 - A|801 }A-2 - -1
2X-RAY DIFFRACTION1{ A|-2 - A|-1 A|706 - A|791 A|801 - A|801 }A706 - 791
3X-RAY DIFFRACTION1{ A|-2 - A|-1 A|706 - A|791 A|801 - A|801 }A801
4X-RAY DIFFRACTION2{ B|-2 - B|-1 B|706 - B|791 B|801 - B|802 }B-2 - -1
5X-RAY DIFFRACTION2{ B|-2 - B|-1 B|706 - B|791 B|801 - B|802 }B706 - 791
6X-RAY DIFFRACTION2{ B|-2 - B|-1 B|706 - B|791 B|801 - B|802 }B801 - 802
7X-RAY DIFFRACTION3{ C|-2 - C|-1 C|706 - C|790 C|801 - C|801 }C-2 - -1
8X-RAY DIFFRACTION3{ C|-2 - C|-1 C|706 - C|790 C|801 - C|801 }C706 - 790
9X-RAY DIFFRACTION3{ C|-2 - C|-1 C|706 - C|790 C|801 - C|801 }C801
10X-RAY DIFFRACTION4{ D|-2 - D|-1 D|706 - D|791 D|801 - D|801 }D-2 - -1
11X-RAY DIFFRACTION4{ D|-2 - D|-1 D|706 - D|791 D|801 - D|801 }D706 - 791
12X-RAY DIFFRACTION4{ D|-2 - D|-1 D|706 - D|791 D|801 - D|801 }D801
13X-RAY DIFFRACTION5{ E|-2 - E|-1 E|706 - E|791 E|801 - E|802 }E-2 - -1
14X-RAY DIFFRACTION5{ E|-2 - E|-1 E|706 - E|791 E|801 - E|802 }E706 - 791
15X-RAY DIFFRACTION5{ E|-2 - E|-1 E|706 - E|791 E|801 - E|802 }E801 - 802
16X-RAY DIFFRACTION6{ F|-2 - F|-1 F|706 - F|790 F|801 - F|801 }F-2 - -1
17X-RAY DIFFRACTION6{ F|-2 - F|-1 F|706 - F|790 F|801 - F|801 }F706 - 790
18X-RAY DIFFRACTION6{ F|-2 - F|-1 F|706 - F|790 F|801 - F|801 }F801

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