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- PDB-5w5a: Crystal structure of Mycobacterium tuberculosis CRP-FNR family tr... -

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Basic information

Entry
Database: PDB / ID: 5w5a
TitleCrystal structure of Mycobacterium tuberculosis CRP-FNR family transcription factor Cmr (Rv1675c)
ComponentsHTH-type transcriptional regulator Cmr
KeywordsTRANSCRIPTION / transcription factor / CRP/FNR family / helix-turn-helix
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold ...helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
HTH-type transcriptional regulator Cmr
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsCheung, J. / Cassidy, M. / Ginter, C. / Ranganathan, S. / Pata, D.J. / McDonough, K.A.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Novel structural features drive DNA binding properties of Cmr, a CRP family protein in TB complex mycobacteria.
Authors: Ranganathan, S. / Cheung, J. / Cassidy, M. / Ginter, C. / Pata, J.D. / McDonough, K.A.
History
DepositionJun 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 9, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulator Cmr
B: HTH-type transcriptional regulator Cmr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9975
Polymers54,7702
Non-polymers2283
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-55 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.615, 92.244, 102.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HTH-type transcriptional regulator Cmr


Mass: 27384.754 Da / Num. of mol.: 2 / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: cmr, MT1714 / Plasmid: modified pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WMH4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.24 Å3/Da / Density % sol: 45.02 % / Mosaicity: 0.254 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG 3350, 0.2M potassium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 7, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 42688 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.069 / Χ2: 1.5 / Net I/σ(I): 11.3 / Num. measured all: 190220
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.85-1.883.60.5420.639198.2
1.88-1.924.50.5290.6751100
1.92-1.954.60.3840.6151100
1.95-1.994.50.3080.6151100
1.99-2.044.50.2630.6561100
2.04-2.084.50.2120.681100
2.08-2.144.60.1890.7221100
2.14-2.194.50.1560.7621100
2.19-2.264.50.1370.8281100
2.26-2.334.60.1260.931100
2.33-2.414.50.1081.0161100
2.41-2.514.50.0981.1481100
2.51-2.634.50.0881.2691100
2.63-2.764.50.0781.381100
2.76-2.944.50.071.6171100
2.94-3.164.50.06121100
3.16-3.484.50.0512.4261100
3.48-3.994.50.0472.8211100
3.99-5.024.40.0453.4861100
5.02-504.20.0565.506199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→41.254 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 22.08
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 4091 5.07 %random
Rwork0.1743 ---
obs0.1762 80614 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.21 Å2 / Biso mean: 34.48 Å2 / Biso min: 6.12 Å2
Refinement stepCycle: final / Resolution: 1.85→41.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 11 338 3833
Biso mean--57.51 39.11 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113627
X-RAY DIFFRACTIONf_angle_d1.274937
X-RAY DIFFRACTIONf_chiral_restr0.057570
X-RAY DIFFRACTIONf_plane_restr0.006653
X-RAY DIFFRACTIONf_dihedral_angle_d13.7061368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8488-1.87050.30381410.28632288242988
1.8705-1.89330.3551680.27262655282399
1.8933-1.91730.3281510.246826542805100
1.9173-1.94250.25751260.230326552781100
1.9425-1.96910.24251160.215426252741100
1.9691-1.99730.21071500.209426732823100
1.9973-2.02710.28391490.20326092758100
2.0271-2.05870.27361270.202826772804100
2.0587-2.09250.26281350.18426492784100
2.0925-2.12860.23971380.195526652803100
2.1286-2.16730.26211660.18426252791100
2.1673-2.2090.20121690.19226252794100
2.209-2.2540.25241560.181726582814100
2.254-2.30310.22781320.182926612793100
2.3031-2.35660.21121530.185726072760100
2.3566-2.41560.21031250.177126782803100
2.4156-2.48090.22931430.176126432786100
2.4809-2.55380.23471440.181726662810100
2.5538-2.63630.22061260.181526302756100
2.6363-2.73050.21951290.182527062835100
2.7305-2.83980.21341530.176426012754100
2.8398-2.9690.20261730.179426292802100
2.969-3.12550.19911420.178226472789100
3.1255-3.32120.19811280.174826712799100
3.3212-3.57750.21371490.156526342783100
3.5775-3.93730.19111350.152626872822100
3.9373-4.50640.15641300.134526592789100
4.5064-5.67520.17341250.147626772802100
5.6752-41.2640.19011120.177226692781100
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)
13.7057-3.08610.11417.79330.51681.4747-0.08260.07150.0371-0.05530.0462-0.0130.03520.08190.03170.1664-0.0402-0.00160.17820.01590.0681-12.9848-10.46852.6348
23.5566-0.09461.26544.6514-0.26435.2407-0.111-0.1245-0.029-0.37030.00680.4927-0.2008-0.35830.09990.1673-0.0471-0.04270.1947-0.03750.2308-21.4877-11.17430.0677
33.2758-0.6022.31250.9772-0.26932.5305-0.0826-0.1882-0.0936-0.03230.07160.14710.1244-0.2020.00910.21-0.0420.04370.1856-0.01620.2204-12.9499-15.34987.1434
45.8903-6.5633.90526.8069-4.33932.6229-0.14080.06420.2970.0661-0.113-0.5525-0.05740.0520.20380.1421-0.0030.04470.19180.01260.1866-2.317-5.42019.2176
54.3675-0.46961.34723.2788-1.37545.9785-0.02130.15990.119-0.1097-0.1087-0.0276-0.04480.11810.13980.29290.0441-0.05340.1653-0.00640.1919-16.632511.4205-2.9454
68.0624.76521.64723.7891-0.23716.7921-0.12780.3798-0.0271-0.4033-0.1587-0.357-0.21290.56820.2850.4210.0474-0.02310.32590.0830.2684-12.143413.2644-11.833
71.9302-0.84080.24941.6817-1.71093.14020.0414-0.07010.1751-0.0005-0.02550.3962-0.05880.2642-0.03880.1586-0.0341-0.0030.2242-0.02280.1717-2.4859.043820.1003
81.49551.0753-1.26232.68961.49225.4251-0.1467-0.1122-0.15910.65650.0219-0.80650.15580.05630.1010.27390.0236-0.13170.35140.0570.316810.4815-7.156932.3727
93.45520.65062.42885.97964.23857.8266-0.0930.27690.04990.06310.0102-1.0583-0.53341.0497-0.13650.2941-0.1014-0.04360.3050.02730.411.34428.595923.6076
100.7125-0.11240.02214.21320.30011.65570.0020.00220.11650.2365-0.0652-0.2577-0.21450.14490.04270.1706-0.012-0.01170.18390.01140.15543.18871.063223.355
114.34961.47591.33533.85450.89666.60950.1234-0.0530.1317-0.3284-0.48230.36790.2794-0.31540.32550.25090.0581-0.02670.2134-0.08480.2787-14.429914.04621.4747
122.6170.0055-2.4256.1185-1.11023.42380.08860.39830.79490.2139-0.72630.7541-0.9518-0.5773-0.23220.4420.1981-0.14180.3367-0.42460.5426-18.792525.375824.3873
136.82532.01991.49482.2779-0.53592.26090.3812-0.5421-0.17650.34-0.64911.10790.1218-0.79830.09120.3081-0.1040.09080.4812-0.28450.6867-20.820716.692330.8715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 62 )A20 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 102 )A63 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 146 )A103 - 146
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 167 )A147 - 167
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 220 )A168 - 220
6X-RAY DIFFRACTION6chain 'A' and (resid 221 through 244 )A221 - 244
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 46 )B19 - 46
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 62 )B47 - 62
9X-RAY DIFFRACTION9chain 'B' and (resid 63 through 76 )B63 - 76
10X-RAY DIFFRACTION10chain 'B' and (resid 77 through 167 )B77 - 167
11X-RAY DIFFRACTION11chain 'B' and (resid 168 through 207 )B168 - 207
12X-RAY DIFFRACTION12chain 'B' and (resid 208 through 220 )B208 - 220
13X-RAY DIFFRACTION13chain 'B' and (resid 221 through 244 )B221 - 244

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