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- PDB-5woq: Crystal structure of an XRE family protein transcriptional regula... -

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Basic information

Entry
Database: PDB / ID: 5woq
TitleCrystal structure of an XRE family protein transcriptional regulator from Mycobacterium smegmatis
ComponentsTranscriptional regulator ClgR
KeywordsTRANSCRIPTION / NIAID / structural genomics / transcription factor / tuberculosis / clgR / resistance / Rv2745c / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator ClgR
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of an XRE family protein transcriptional regulator from Mycobacterium smegmatis
Authors: Edwards, T.E. / Mayclin, S.J. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionAug 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Transcriptional regulator ClgR
B: Transcriptional regulator ClgR
C: Transcriptional regulator ClgR


Theoretical massNumber of molelcules
Total (without water)39,3203
Polymers39,3203
Non-polymers00
Water2,162120
1
A: Transcriptional regulator ClgR

A: Transcriptional regulator ClgR


Theoretical massNumber of molelcules
Total (without water)26,2142
Polymers26,2142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area1620 Å2
ΔGint-11 kcal/mol
Surface area8320 Å2
MethodPISA
2
B: Transcriptional regulator ClgR
C: Transcriptional regulator ClgR


Theoretical massNumber of molelcules
Total (without water)26,2142
Polymers26,2142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-12 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.500, 54.870, 60.090
Angle α, β, γ (deg.)90.000, 117.100, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcriptional regulator ClgR


Mass: 13106.833 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: clgR, MSMEG_2694, MSMEI_2628 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QVU1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.89 Å3/Da / Density % sol: 35.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: MysmA.01657.a.B1.PS38057 at 18.6 mg/mL against JCSG+ F3 0.1 M Tris pH 8.0, 20% MPD, crystal tracking ID 285293f3, unique puck ID quf9-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 23311 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.986 % / Biso Wilson estimate: 34.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.031 / Net I/σ(I): 26.54
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.018 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 3.17 / Num. unique obs: 1720 / CC1/2: 0.893 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(1.12_2829)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F51

3f51


Resolution: 1.95→31.74 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.01
RfactorNum. reflection% reflection
Rfree0.2365 1978 8.49 %
Rwork0.1919 --
obs0.1958 23304 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.76 Å2 / Biso mean: 50.0117 Å2 / Biso min: 20.69 Å2
Refinement stepCycle: final / Resolution: 1.95→31.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 0 120 1949
Biso mean---48.57 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061926
X-RAY DIFFRACTIONf_angle_d0.7132624
X-RAY DIFFRACTIONf_chiral_restr0.041320
X-RAY DIFFRACTIONf_plane_restr0.003355
X-RAY DIFFRACTIONf_dihedral_angle_d22.6751246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94750.29821140.268415431657100
1.9475-2.00010.31671430.263314921635100
2.0001-2.0590.30251400.24415461686100
2.059-2.12540.27761340.240615021636100
2.1254-2.20140.27781610.218315081669100
2.2014-2.28950.26371330.218215091642100
2.2895-2.39370.28761260.224315451671100
2.3937-2.51980.28351300.203515191649100
2.5198-2.67760.24771560.206815011657100
2.6776-2.88420.25931470.208615281675100
2.8842-3.17420.21851540.190515051659100
3.1742-3.6330.23361440.177115291673100
3.633-4.5750.1921470.152715361683100
4.575-31.74430.22011490.18331563171299
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)
19.8181-6.5129-6.78088.46916.11695.41350.7068-0.62470.7441-0.91690.0486-0.7222-1.00990.7207-0.66730.3493-0.04060.01580.3102-0.01640.276815.846-23.3206-15.7957
23.55182.094-0.07275.4112-1.23725.450.3743-0.9694-0.07890.0268-0.20570.31240.3455-0.2706-0.14670.3462-0.0366-0.03250.29080.06540.3088.127-31.8088-10.5939
39.8897-6.34581.51725.2018-1.4030.40740.34350.34410.0982-0.44590.1444-0.33630.51030.69690.03410.39590.03330.09940.38240.02950.371918.078-32.1475-17.4537
45.0112-1.4463-2.86357.24094.66063.903-0.0936-0.0024-0.1992-0.3645-0.11840.04270.0831-0.06650.17230.3346-0.04090.00610.33790.04640.21263.9985-25.1166-19.1201
52.33350.059-4.11132.896-0.66429.30820.5226-1.46090.41840.4495-0.1319-0.277-1.22180.9548-0.36860.5003-0.08980.02430.4021-0.04020.340217.1079-15.9783-22.6404
65.42091.9248-3.33618.1243-2.64586.9403-0.02020.4990.0065-0.33290.1315-0.1004-0.00890.007-0.08090.2029-0.0046-0.00630.3493-0.0230.1849.024-17.14190.0523
78.09010.6826-0.60638.8518-1.33998.37420.1871-0.8054-0.46850.2153-0.2059-0.0940.46730.53010.01410.2089-0.01180.00810.29820.01940.19117.0367-22.545810.1466
85.36752.9249-3.64185.27130.29947.24710.2749-0.4477-0.2316-0.1110.0708-0.0982-0.20190.5962-0.34180.1892-0.0531-0.0140.332-0.09110.280415.4794-14.48640.2642
92.91810.6781-1.46366.31241.05121.19220.6269-0.69821.34720.2260.3064-0.4724-0.97810.641-0.6150.7678-0.31270.30440.617-0.25980.783916.76435.52724.6423
100.6564-0.1118-0.29781.6225-0.13641.55310.7871-0.76580.83480.34180.42240.2583-1.1590.5271-0.35890.916-0.35630.34550.3946-0.30580.767610.50462.8135.3925
113.4514-2.68384.20685.4817-2.39556.2814-0.68490.31190.21460.26490.7124-1.1393-0.35220.5833-0.00680.3952-0.12390.05580.643-0.31620.656625.7849-8.56643.5188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 20 )A2 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 42 )A21 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 49 )A43 - 49
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 63 )A50 - 63
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 81 )A64 - 81
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 19 )B1 - 19
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 49 )B20 - 49
8X-RAY DIFFRACTION8chain 'B' and (resid 50 through 85 )B50 - 85
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 31 )C3 - 31
10X-RAY DIFFRACTION10chain 'C' and (resid 32 through 63 )C32 - 63
11X-RAY DIFFRACTION11chain 'C' and (resid 64 through 85 )C64 - 85

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