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- PDB-7sjy: Crystal structure of Clostridium thermocellum RsgI9 S1C-NTF2 bi-domain -

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Basic information

Entry
Database: PDB / ID: 7sjy
TitleCrystal structure of Clostridium thermocellum RsgI9 S1C-NTF2 bi-domain
ComponentsAnti-sigma-I factor RsgI9
KeywordsHYDROLASE / ANTI-SIGMA FACTOR / S1C PEPTIDASE / NTF2-LIKE
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / plasma membrane
Similarity search - Function
Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Peptidase S1C / Trypsin-like peptidase domain / Peptidase S1, PA clan
Similarity search - Domain/homology
Anti-sigma-I factor RsgI9
Similarity search - Component
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMahoney, B.J. / Cascio, D. / Clubb, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
CitationJournal: Proteins / Year: 2022
Title: The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism of biomass sensing.
Authors: Mahoney, B.J. / Takayesu, A. / Zhou, A. / Cascio, D. / Clubb, R.T.
History
DepositionOct 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 15, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-sigma-I factor RsgI9
B: Anti-sigma-I factor RsgI9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,37215
Polymers69,1752
Non-polymers1,19713
Water3,459192
1
A: Anti-sigma-I factor RsgI9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1407
Polymers34,5871
Non-polymers5536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anti-sigma-I factor RsgI9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2328
Polymers34,5871
Non-polymers6457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.630, 78.060, 81.210
Angle α, β, γ (deg.)90.000, 112.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Anti-sigma-I factor RsgI9


Mass: 34587.289 Da / Num. of mol.: 2 / Fragment: RsgI9
Source method: isolated from a genetically manipulated source
Details: N-terminal Gly scar after TEV cleavage of tags. Expressed construct comprises amino acid residues 387-702 of the full-length Anti-sigma-I factor RsgI9.
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Gene: rsgi9 / Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3DC20
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Fragment: GOL / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG-3350, 20 mM HEPES, 2 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97903 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2→74.77 Å / Num. obs: 48797 / % possible obs: 98.4 % / Redundancy: 5.056 % / Biso Wilson estimate: 40.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.055 / Χ2: 0.922 / Net I/σ(I): 16.51 / Num. measured all: 246720 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.054.8630.6182.617477365935940.8390.69598.2
2.05-2.115.1050.483.4217719351734710.9030.53898.7
2.11-2.175.2190.3594.5818007347434500.9490.40199.3
2.17-2.245.1490.2895.616936333932890.960.32398.5
2.24-2.314.9990.236.7816093328232190.9730.25898.1
2.31-2.394.6060.1927.6414121314930660.9750.21897.4
2.39-2.485.3250.1689.4616103304330240.9870.18799.4
2.48-2.585.3590.1411.1215729294429350.990.15699.7
2.58-2.75.2450.11312.9714722281728070.9940.12799.6
2.7-2.835.1640.09215.6713751268226630.9950.10399.3
2.83-2.985.1980.06819.8713140256025280.9970.07698.8
2.98-3.165.0620.05324.0212006241923720.9970.0698.1
3.16-3.384.7090.04427.6510392231322070.9980.0595.4
3.38-3.654.8040.03833.069848210620500.9980.04397.3
3.65-45.1410.03537.0710055198219560.9990.03998.7
4-4.475.0150.03441.128691176217330.9980.03898.4
4.47-5.164.9950.03141.487807159215630.9980.03598.2
5.16-6.324.8360.03140.076180133312780.9990.03595.9
6.32-8.944.9330.02642.254943103610020.9990.0396.7
8.94-74.775.0850.02446.4730005995900.9990.02798.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å74.77 Å
Translation2 Å74.77 Å

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Processing

Software
NameVersionClassification
BUSTERrefinement
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6L

5b6l


Resolution: 2→74.77 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.173 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 4880 10 %RANDOM
Rwork0.2102 ---
obs0.2126 48797 98.5 %-
Displacement parametersBiso max: 120.6 Å2 / Biso mean: 51.48 Å2 / Biso min: 25.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.6905 Å20 Å27.4027 Å2
2--2.1362 Å20 Å2
3---0.5544 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2→74.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4777 0 78 192 5047
Biso mean--64.06 48.13 -
Num. residues----625
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1728SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes822HARMONIC5
X-RAY DIFFRACTIONt_it4921HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion664SEMIHARMONIC5
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_contact3783SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4921HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg6633HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion14.27
LS refinement shellResolution: 2→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3464 98 10.04 %
Rwork0.3244 878 -
all0.3266 976 -
obs--96.83 %
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)
11.7082-0.22330.79871.65840.26551.853-0.1016-0.01740.04510.1381-0.046-0.0757-0.21640.08030.14760.0679-0.0341-0.17-0.19780.028-0.0198-32.625227.982667.4065
21.8572-0.59261.0193.0728-0.42845.1-0.0033-0.05120.15040.1944-0.215-0.82590.14880.97360.2183-0.10310.0031-0.2234-0.01220.15850.1274-5.5515.904674.275
32.3406-0.14391.4751.0487-0.16122.2581-0.06210.26130.0451-0.0877-0.0751-0.3468-0.07730.28210.1372-0.0897-0.0218-0.0513-0.13260.02970.1425-24.69336.092336.7849
40.6520.06180.49991.78410.71231.29630.0505-0.03270.0191-0.0937-0.03410.205-0.0055-0.0818-0.01640.0056-0.0004-0.1072-0.10970.00660.0367-54.436111.445234.3519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|389 - 595}A389 - 595
2X-RAY DIFFRACTION2{A|596 - 702}A596 - 702
3X-RAY DIFFRACTION3{B|389 - 595}B389 - 595
4X-RAY DIFFRACTION4{B|596 - 702}B596 - 702

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