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- PDB-5w5b: Crystal structure of Mycobacterium tuberculosis CRP-FNR family tr... -

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Basic information

Entry
Database: PDB / ID: 5w5b
TitleCrystal structure of Mycobacterium tuberculosis CRP-FNR family transcription factor Cmr (Rv1675c), truncated construct
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1152
Polymers26,0791
Non-polymers351
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.109, 72.530, 53.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HTH-type transcriptional regulator Cmr


Mass: 26079.215 Da / Num. of mol.: 1 / Fragment: unp residues 13-244 / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: cmr, MT1714 / Plasmid: modified pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WMH4
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.07 Å3/Da / Density % sol: 40.59 % / Mosaicity: 0.673 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1M di-ammonium hydrogen phosphate, 0.1M imidazole, 0.2M NaCl

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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 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 20631 / % possible obs: 99.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.057 / Χ2: 1.339 / Net I/σ(I): 14.7 / Num. measured all: 107589
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.8-1.833.10.6470.515194.1
1.83-1.863.70.6140.499198.5
1.86-1.94.20.5620.5491100
1.9-1.944.60.4210.5351100
1.94-1.984.60.3190.521100
1.98-2.034.70.250.5451100
2.03-2.084.70.2030.5861100
2.08-2.134.70.1660.5611100
2.13-2.24.70.1430.6351100
2.2-2.274.70.1250.7071100
2.27-2.354.70.1080.7361100
2.35-2.444.70.0910.8551100
2.44-2.554.70.0860.9621100
2.55-2.694.70.0731.0391100
2.69-2.864.70.0641.326199.9
2.86-3.084.60.0581.69199.8
3.08-3.394.70.0491.722199.5
3.39-3.884.60.0431.852199.4
3.88-4.887.70.0481.978198.9
4.88-5014.30.0572.8771100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
RESOLVE2.15phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.8→43.88 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.07 / Phase error: 23.24
RfactorNum. reflection% reflection
Rfree0.2185 1977 5.12 %
Rwork0.1733 --
obs0.1755 38639 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.78 Å2 / Biso mean: 45.6 Å2 / Biso min: 23.48 Å2
Refinement stepCycle: final / Resolution: 1.8→43.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 1 90 1822
Biso mean--50.03 48.23 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011767
X-RAY DIFFRACTIONf_angle_d1.292399
X-RAY DIFFRACTIONf_chiral_restr0.053279
X-RAY DIFFRACTIONf_plane_restr0.006315
X-RAY DIFFRACTIONf_dihedral_angle_d13.251664
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 (%)
1.7948-1.83970.35421220.30482254237686
1.8397-1.88940.29431530.27526482801100
1.8894-1.9450.26671500.259226152765100
1.945-2.00780.26431390.220226832822100
2.0078-2.07960.29961610.210826232784100
2.0796-2.16280.23551750.19626212796100
2.1628-2.26130.231520.200126352787100
2.2613-2.38050.2751310.188526452776100
2.3805-2.52960.23541120.188726742786100
2.5296-2.72490.19141470.190126432790100
2.7249-2.99910.25841430.18726672810100
2.9991-3.43290.25481430.182126232766100
3.4329-4.32450.18511510.144526392790100
4.3245-43.89280.1619980.141826922790100
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)
10.96820.0542-0.32273.0269-0.93293.8695-0.1130.1569-0.0763-0.18780.1024-0.02370.1024-0.10770.02470.1713-0.01790.01960.2249-0.00040.2444-7.562921.981521.4882
21.72121.4264-0.78414.8932-0.82842.2481-0.1192-0.0263-0.0923-0.12780.13460.04240.2092-0.05230.00830.23930.0017-0.00320.25420.00570.2897-6.303724.229520.4649
36.36880.64641.01534.5311-0.34936.02740.0352-0.15320.33870.0026-0.05180.2292-0.1781-0.31950.01410.27750.0079-0.00530.2914-0.05940.2608-14.227231.280743.938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 76 )A21 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 167 )A77 - 167
3X-RAY DIFFRACTION3chain 'A' and (resid 168 through 244 )A168 - 244

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