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- PDB-5xe7: Crystal structure of Mycobacterium tuberculosis extracytoplasmic ... -

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Basic information

Entry
Database: PDB / ID: 5xe7
TitleCrystal structure of Mycobacterium tuberculosis extracytoplasmic function sigma factor SigJ
ComponentsECF RNA polymerase sigma factor SigJ
KeywordsDNA BINDING PROTEIN / RNA polymerase subunit / ECF41 sigma factor / DNA binding / SnoaL_2 domain
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / response to hydrogen peroxide / DNA binding
Similarity search - Function
: / PhyR, sigma-like (SL) domain / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain ...: / PhyR, sigma-like (SL) domain / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Winged helix-like DNA-binding domain superfamily / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ECF RNA polymerase sigma factor SigJ
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.162 Å
AuthorsGoutam, K. / Gopal, B.
Funding support India, 2items
OrganizationGrant numberCountry
department of biotechnology, India India
Department of science and technology India
Citation
Journal: Nucleic Acids Res. / Year: 2017
Title: The fused SnoaL_2 domain in the Mycobacterium tuberculosis sigma factor sigma J modulates promoter recognition
Authors: Goutam, K. / Gupta, A.K. / Gopal, B.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Crystallographic studies of the extracytoplasmic function sigma factor sigma(J) from Mycobacterium tuberculosis.
Authors: Goutam, K. / Gupta, A.K. / Gopal, B.
History
DepositionApr 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ECF RNA polymerase sigma factor SigJ
B: ECF RNA polymerase sigma factor SigJ


Theoretical massNumber of molelcules
Total (without water)67,4202
Polymers67,4202
Non-polymers00
Water3,243180
1
A: ECF RNA polymerase sigma factor SigJ


Theoretical massNumber of molelcules
Total (without water)33,7101
Polymers33,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ECF RNA polymerase sigma factor SigJ


Theoretical massNumber of molelcules
Total (without water)33,7101
Polymers33,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: ECF RNA polymerase sigma factor SigJ

A: ECF RNA polymerase sigma factor SigJ


Theoretical massNumber of molelcules
Total (without water)67,4202
Polymers67,4202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area1410 Å2
ΔGint-14 kcal/mol
Surface area25410 Å2
MethodPISA
4
B: ECF RNA polymerase sigma factor SigJ

B: ECF RNA polymerase sigma factor SigJ


Theoretical massNumber of molelcules
Total (without water)67,4202
Polymers67,4202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area1450 Å2
ΔGint-16 kcal/mol
Surface area26750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.457, 133.599, 133.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein ECF RNA polymerase sigma factor SigJ / ECF sigma factor SigJ / Alternative RNA polymerase sigma factor SigJ / RNA polymerase sigma-J ...ECF sigma factor SigJ / Alternative RNA polymerase sigma factor SigJ / RNA polymerase sigma-J factor / Sigma-J factor


Mass: 33710.184 Da / Num. of mol.: 2 / Fragment: UNP residues 1-306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: sigJ, Rv3328c / Production host: Escherichia coli (E. coli) / References: UniProt: L0TCG5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 0.2M potassium sodium tartrate, 0.1M sodium citrate tribasic pH 5.6, 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97867 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97867 Å / Relative weight: 1
ReflectionResolution: 2.16→66.8 Å / Num. obs: 35959 / % possible obs: 99.9 % / Redundancy: 22.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 25.1
Reflection shellResolution: 2.16→2.28 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 5166 / CC1/2: 0.938 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.162→66.749 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.75
Details: The structure factor file contains friedel pairs in F_PLUS/MINUS and I_PLUS/MINUS columns. The difference between the reflection number for data collection and refinement is because of ...Details: The structure factor file contains friedel pairs in F_PLUS/MINUS and I_PLUS/MINUS columns. The difference between the reflection number for data collection and refinement is because of differential usage of anomalous reflection pairs by the two programs scala (counting the pair as one reflection) and phenix.refine (counting the pair as separate reflection).
RfactorNum. reflection% reflection
Rfree0.2702 3493 5.09 %
Rwork0.257 --
obs0.261 65274 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.162→66.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 0 180 3985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043876
X-RAY DIFFRACTIONf_angle_d0.8545336
X-RAY DIFFRACTIONf_dihedral_angle_d12.4561221
X-RAY DIFFRACTIONf_chiral_restr0.031664
X-RAY DIFFRACTIONf_plane_restr0.005700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1622-2.19950.4021700.38193279X-RAY DIFFRACTION94
2.1995-2.23950.38741650.35813204X-RAY DIFFRACTION95
2.2395-2.28250.33762060.35263272X-RAY DIFFRACTION94
2.2825-2.32910.39871960.36943248X-RAY DIFFRACTION94
2.3291-2.37970.34331820.36323252X-RAY DIFFRACTION95
2.3797-2.43510.34991680.33443279X-RAY DIFFRACTION95
2.4351-2.4960.3541960.35243207X-RAY DIFFRACTION94
2.496-2.56340.38051640.33813314X-RAY DIFFRACTION95
2.5634-2.63880.30622020.32613220X-RAY DIFFRACTION94
2.6388-2.72390.3551320.31733301X-RAY DIFFRACTION96
2.7239-2.82120.30191420.30753351X-RAY DIFFRACTION96
2.8212-2.93410.36622000.29483188X-RAY DIFFRACTION94
2.9341-3.06750.31022000.28423252X-RAY DIFFRACTION94
3.0675-3.22910.26271700.28423265X-RAY DIFFRACTION95
3.2291-3.43120.28071720.26793262X-RAY DIFFRACTION95
3.4312-3.69570.24561380.24963322X-RAY DIFFRACTION96
3.6957-4.0670.26971740.22483263X-RAY DIFFRACTION95
4.067-4.65380.20471830.19653262X-RAY DIFFRACTION95
4.6538-5.85720.19431840.20993254X-RAY DIFFRACTION95
5.8572-31.4810.27491490.22233235X-RAY DIFFRACTION94
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)
10.3036-0.1395-0.063-0.0053-0.01110.00470.1282-0.67940.3147-0.264-0.27140.13050.26180.0233-0.13920.2536-0.07030.06790.32630.02440.4227-17.5361-21.8942-27.0809
20.0986-0.13580.06040.06060.00790.04570.5502-0.06050.1623-0.2291-0.5018-0.10410.03630.1064-0.00170.312-0.09130.09040.32830.00350.4782-10.1644-24.7591-28.4874
30.03130.05960.01530.04210.02210.05920.04450.10780.0733-0.15590.06630.2317-0.16490.27750.00420.34590.01550.09290.33750.0510.3237-20.4722-28.3247-12.0893
4-0.00470.222-0.11230.26240.0996-0.06050.1867-0.3856-0.07080.03140.07190.095-0.03320.62420.20040.25070.06570.05090.56530.0080.394-12.3389-38.2716-18.595
50.04060.00450.08510.0575-0.1040.08310.06550.39880.1163-0.2228-0.10970.07030.4380.2478-0.00020.52560.00310.04940.58060.00350.3854-21.6001-34.44155.7406
60.33520.40880.25510.06970.14640.15030.06470.01130.08450.0186-0.1127-0.0950.06290.4519-0.32910.41730.00160.04480.4520.02470.3477-24.9725-27.34182.3067
70.10240.0077-0.05590.02620.02160.0719-0.10380.19020.09450.1321-0.0538-0.1905-0.1541-0.0703-0.00010.36750.0377-0.02150.40590.01130.4868-19.8761-40.261-43.5993
80.2579-0.2188-0.0658-0.0285-0.13590.20250.0698-0.1494-0.0304-0.27320.0132-0.04320.0571-0.10240.02280.32830.0929-0.02720.28850.02440.5214-21.1351-46.0124-40.1705
9-0.0024-0.03010.03820.0453-0.06250.05520.23360.226-0.34570.4505-0.2295-0.2209-0.0513-0.2648-0.00030.53750.43610.2077-0.1310.03020.7694-25.1315-52.5669-30.5128
100.36350.38890.33640.76220.3350.4413-0.02850.1382-0.04410.24560.05680.38550.14440.04420.64140.32830.01380.06070.2305-0.01810.3754-20.7549-51.2297-26.5497
110.1537-0.00360.08640.06210.02360.03150.2430.143-0.09360.0442-0.07780.3264-0.36310.180.00190.55380.0290.04640.2144-0.00240.6361-14.7468-73.4649-34.7851
121.25970.4410.45620.33920.01520.1863-0.36870.73770.12530.01370.45930.6210.20590.19780.05990.49770.11340.0920.01840.09990.6691-12.6834-65.4433-40.5219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:44)A2 - 44
2X-RAY DIFFRACTION2(chain A and resid 45:73)A45 - 73
3X-RAY DIFFRACTION3(chain A and resid 74:112)A74 - 112
4X-RAY DIFFRACTION4(chain A and resid 113:181)A113 - 181
5X-RAY DIFFRACTION5(chain A and resid 182:212)A182 - 212
6X-RAY DIFFRACTION6(chain A and resid 213:297)A213 - 297
7X-RAY DIFFRACTION7(chain B and resid 2:40)B2 - 40
8X-RAY DIFFRACTION8(chain B and resid 44:100)B44 - 100
9X-RAY DIFFRACTION9(chain B and resid 101:121)B101 - 121
10X-RAY DIFFRACTION10(chain B and resid 122:187)B122 - 187
11X-RAY DIFFRACTION11(chain B and resid 188:242)B188 - 242
12X-RAY DIFFRACTION12(chain B and resid 243:297)B243 - 297

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