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- PDB-2nyx: Crystal structure of RV1404 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 2nyx
TitleCrystal structure of RV1404 from Mycobacterium tuberculosis
ComponentsProbable transcriptional regulatory protein, Rv1404
KeywordsTRANSCRIPTION / alpha/beta / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC / Integrated Center for Structure and Function Innovation / ISFI
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Probable transcriptional regulatory protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsYu, M. / Bursey, E.H. / Radhakannan, R. / Kim, C.-Y. / Kaviratne, T. / Woodruff, T. / Segelke, B.W. / Lekin, T. / Toppani, D. / Terwilliger, T.C. ...Yu, M. / Bursey, E.H. / Radhakannan, R. / Kim, C.-Y. / Kaviratne, T. / Woodruff, T. / Segelke, B.W. / Lekin, T. / Toppani, D. / Terwilliger, T.C. / Hung, L.-W. / TB Structural Genomics Consortium (TBSGC) / Integrated Center for Structure and Function Innovation (ISFI)
CitationJournal: To be Published
Title: Crystal structure of RV1404 from Mycobacterium tuberculosis
Authors: Yu, M. / Bursey, E.H. / Radhakannan, R. / Kim, C.-Y. / Kaviratne, T. / Woodruff, T. / Segelke, B.W. / Lekin, T. / Toppani, D. / Terwilliger, T.C. / Hung, L.-W.
History
DepositionNov 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable transcriptional regulatory protein, Rv1404
B: Probable transcriptional regulatory protein, Rv1404
C: Probable transcriptional regulatory protein, Rv1404
D: Probable transcriptional regulatory protein, Rv1404


Theoretical massNumber of molelcules
Total (without water)75,2154
Polymers75,2154
Non-polymers00
Water2,558142
1
A: Probable transcriptional regulatory protein, Rv1404
B: Probable transcriptional regulatory protein, Rv1404


Theoretical massNumber of molelcules
Total (without water)37,6082
Polymers37,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-44 kcal/mol
Surface area14690 Å2
MethodPISA
2
C: Probable transcriptional regulatory protein, Rv1404
D: Probable transcriptional regulatory protein, Rv1404


Theoretical massNumber of molelcules
Total (without water)37,6082
Polymers37,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-47 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.262, 54.747, 227.505
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is likely to be a homodimer. The asymmetric unit contain two such dimers.

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Components

#1: Protein
Probable transcriptional regulatory protein, Rv1404


Mass: 18803.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1404 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P71672
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22.0% PEG 3350, 0.2 M Potassium Thiocyanate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2006 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
9.2172367220.1461.342.32574387.8
7.624.3898310.211.042.91174677.6
9.136.42001050.1551.282.32201874.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955010010.0771.44811.1
3.934.9510010.0951.57611.3
3.443.9310010.1391.64111.5
3.123.4410010.1891.39811.5
2.93.1210010.281.21311.4
2.732.910010.3531.1059.6
2.592.7395.410.391.036.9
2.482.5981.610.4180.9784.8
2.382.4860.810.4720.8893.7
2.32.3838.510.5460.8973
6.245010020.1050.88710.9
4.966.2499.220.2721.02210.5
4.334.9698.920.1971.2399.7
3.944.3398.520.2481.0749.3
3.653.9494.720.3441.0668.2
3.443.6589.520.4221.0285.8
3.273.4477.320.4010.9353.6
3.123.2756.720.4531.0242.5
33.1236.720.6210.8432
2.9319.420.5670.7751.7
4.955010030.0781.18711.2
3.934.9510030.1081.50911.6
3.443.9310030.171.48911.9
3.123.4410030.2581.30811.8
2.93.1299.830.3761.0910.2
2.732.993.530.4521.0036.2
2.592.7371.230.450.9423.7
2.482.5941.230.460.8922.7
2.382.4823.130.5640.82.2
2.32.3812.130.6120.8131.8
ReflectionResolution: 2.3→19.8 Å / Num. all: 29320 / Num. obs: 25743 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.146 / Χ2: 1.343 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3830.54611050.897138.5
2.38-2.483.70.47217570.889160.8
2.48-2.594.80.41823510.978181.6
2.59-2.736.90.3927461.03195.4
2.73-2.99.60.35328751.1051100
2.9-3.1211.40.2828981.2131100
3.12-3.4411.50.18929411.3981100
3.44-3.9311.50.13929411.6411100
3.93-4.9511.30.09529701.5761100
4.95-5011.10.07731591.4481100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→19.8 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.855 / SU B: 18.773 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.626 / ESU R Free: 0.293
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1179 5.1 %RANDOM
Rwork0.229 ---
all0.231 22960 --
obs0.231 22960 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.882 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å20 Å2
2--0.49 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 0 142 4602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224512
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9756136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2355582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89122.083192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.56315778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8751562
X-RAY DIFFRACTIONr_chiral_restr0.1230.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023326
X-RAY DIFFRACTIONr_nbd_refined0.2310.22288
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.25
X-RAY DIFFRACTIONr_mcbond_it0.7361.53003
X-RAY DIFFRACTIONr_mcangle_it1.04724732
X-RAY DIFFRACTIONr_scbond_it1.46631600
X-RAY DIFFRACTIONr_scangle_it2.624.51404
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 28 -
Rwork0.254 340 -
obs-368 100 %
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)
12.37181.8646-0.10753.5704-0.20691.4957-0.0104-0.0026-0.1095-0.04160.0277-0.2125-0.02220.1283-0.0173-0.14580.04430.0058-0.0197-0.0121-0.165479.462368.8299273.9606
20.971-0.11090.34483.0467-2.04074.9529-0.04620.0455-0.0225-0.09450.0083-0.04610.06020.16210.0379-0.202-0.0113-0.0028-0.1237-0.0308-0.132569.81762.4187262.8056
32.3131.9420.26123.4861-0.10791.38190.07790.00220.1821-0.0607-0.01970.0446-0.0809-0.0563-0.0583-0.10480.04740.0225-0.1979-0.0129-0.218451.313643.8561237.9724
42.44790.16031.77582.00730.17715.80930.0061-0.13-0.00360.0706-0.03710.0061-0.19930.02360.031-0.179-0.0170.0359-0.23620.0124-0.165845.462333.8745249.3615
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA7 - 1527 - 152
22BB10 - 15610 - 156
33CC7 - 1527 - 152
44DD10 - 15610 - 156

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