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- PDB-3h87: Rv0301 Rv0300 Toxin Antitoxin Complex from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3h87
TitleRv0301 Rv0300 Toxin Antitoxin Complex from Mycobacterium tuberculosis
Components(Putative uncharacterized ...) x 2
KeywordsTOXIN/ANTITOXIN / toxin antitoxin complex / VapBC complex / RHH motif / structural genomics / tuberculosis / Integrated Center for Structure and Function Innovation / ISFI / TOXIN-ANTITOXIN COMPLEX / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


negative regulation of ribonuclease activity / RNA nuclease activity / positive regulation of translation / Hydrolases; Acting on ester bonds / negative regulation of translation / regulation of DNA-templated transcription / magnesium ion binding
Similarity search - Function
PIN domain / VapC family / Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / Met repressor-like / Arc Repressor Mutant / 5'-nuclease / Arc-type ribbon-helix-helix / Ribbon-helix-helix / PIN domain ...PIN domain / VapC family / Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / Met repressor-like / Arc Repressor Mutant / 5'-nuclease / Arc-type ribbon-helix-helix / Ribbon-helix-helix / PIN domain / PIN-like domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / IMIDAZOLE / Antitoxin VapB2 / Ribonuclease VapC2 / Ribonuclease VapC2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.49 Å
AuthorsMin, A. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. / Integrated Center for Structure and Function Innovation (ISFI)
CitationJournal: Protein Sci. / Year: 2012
Title: The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin-antitoxin complex from M. tuberculosis reveals a Mg(2+) ion in the active site and a putative RNA-binding site.
Authors: Min, A.B. / Miallau, L. / Sawaya, M.R. / Habel, J. / Cascio, D. / Eisenberg, D.
History
DepositionApr 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 7, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,00612
Polymers51,3744
Non-polymers6328
Water7,837435
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,01324
Polymers102,7498
Non-polymers1,26416
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)85.557, 85.557, 155.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-268-

HOH

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Components

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Putative uncharacterized ... , 2 types, 4 molecules ABCD

#1: Protein Putative uncharacterized protein


Mass: 17586.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Rv0301 Toxin / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT0314, Rv0301 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: O07228, UniProt: P9WFB9*PLUS
#2: Protein Putative uncharacterized protein


Mass: 8100.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Rv0300 Antitoxin / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0300 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: O07227

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Non-polymers , 5 types, 443 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 298 K / pH: 7
Details: 200mM Potassium Acetate, 7.5% PEG-3350, 50mM Tris, 500mM NaCl, 140mM Imidazole, 10mM TCEP, beta-mercaptoethanol, pH 7.0, microbatch, under oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 11.3 % / Av σ(I) over netI: 36.9 / Number: 1030128 / Rmerge(I) obs: 0.083 / Χ2: 0.98 / D res high: 1.85 Å / D res low: 80 Å / Num. obs: 91363 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.998099.910.0440.9911.4
3.163.9910010.060.97711.3
2.763.1610010.0781.03611.3
2.512.7610010.0840.93611.2
2.332.5110010.0951.02711.2
2.192.3310010.1160.97511.2
2.082.1910010.1520.95511.3
1.992.0810010.2010.97811.3
1.921.9910010.2780.98911.3
1.851.9210010.40.94411.3
ReflectionResolution: 1.49→80 Å / Num. all: 94698 / Num. obs: 94698 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.05 / Χ2: 1.004 / Net I/σ(I): 36.9
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 4 / Num. unique all: 9323 / Χ2: 1.001 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 68029
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.94-10022.70.653527
6.32-8.9427.60.865859
5.16-6.3232.60.8511077
4.47-5.1625.40.8941262
4-4.4722.60.9211403
3.65-423.50.9011558
3.38-3.6524.20.9081649
3.16-3.3825.30.9011796
2.98-3.1625.30.9041897
2.83-2.9825.40.8951977
2.7-2.8325.40.8992110
2.58-2.724.80.9062180
2.48-2.5824.70.9062263
2.39-2.48250.92357
2.31-2.39230.9112426
2.24-2.3123.90.9042512
2.17-2.2424.10.9092573
2.11-2.1724.10.8992678
2.05-2.11240.8992732
2-2.0523.90.92795
1.95-224.30.8852858
1.91-1.9524.20.8692943
1.86-1.9124.90.8723019
1.83-1.86250.8573072
1.79-1.8326.60.8373099
1.75-1.79270.8243184
1.72-1.7527.80.8053239
1.69-1.7229.10.7813303
1.65-1.6931.30.7344681

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.49→60.52 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.176 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.912 / SU B: 1.528 / SU ML: 0.03 / SU R Cruickshank DPI: 0.054 / SU Rfree: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.174 4796 5.1 %RANDOM
Rwork0.156 ---
obs0.157 94557 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 58.78 Å2 / Biso mean: 20.866 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.49→60.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 40 435 3753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213421
X-RAY DIFFRACTIONr_bond_other_d0.0010.022430
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9864640
X-RAY DIFFRACTIONr_angle_other_deg0.87435849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9535432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.58421.553161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23715598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4491555
X-RAY DIFFRACTIONr_chiral_restr0.0910.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213790
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02725
X-RAY DIFFRACTIONr_mcbond_it1.76622114
X-RAY DIFFRACTIONr_mcbond_other0.5552846
X-RAY DIFFRACTIONr_mcangle_it2.78233417
X-RAY DIFFRACTIONr_scbond_it2.73221307
X-RAY DIFFRACTIONr_scangle_it4.25231215
LS refinement shellResolution: 1.49→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 334 -
Rwork0.213 6586 -
all-6920 -
obs--99.99 %
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)
12.53090.1477-0.07390.89560.34052.3094-0.09550.373-0.1832-0.20330.0494-0.00920.1021-0.05310.046-0.1223-0.04080.0104-0.0995-0.0242-0.183638.78318.17933.22
21.1453-0.029-0.36810.71270.10211.4731-0.05940.0855-0.1084-0.0854-0.00050.10190.1252-0.17050.0599-0.2116-0.0269-0.0016-0.1330.0038-0.175830.13819.67647.195
31.1913-0.35740.13340.82780.46332.7472-0.0409-0.14870.04520.1230.0882-0.01410.06710.1154-0.0473-0.22430.0289-0.0013-0.14570.0007-0.216851.30627.78869.893
41.90360.5446-0.08531.23880.58731.2383-0.0209-0.0647-0.11240.1298-0.04130.08440.1018-0.10840.0622-0.2020.00970.008-0.17710.0144-0.206337.20824.64865.636
51.0435-0.2834-1.22230.59850.41892.9304-0.08760.0308-0.0158-0.02540.0187-0.08420.15790.14340.0689-0.21390.00650.014-0.17970.0041-0.198449.54225.92250.271
61.1994-0.052-0.15641.3178-0.18461.816-0.0308-0.0081-0.0542-0.0232-0.0092-0.0790.06490.1370.04-0.24170.01170.0098-0.18130.0102-0.213854.27824.6854.899
72.943-0.6289-0.90494.8768-1.242113.2878-0.2276-0.3405-0.25080.54670.1164-0.10890.96540.40620.1112-0.09010.0802-0.0055-0.02850.0146-0.143458.63821.11869.681
844.132227.40515.699532.42397.95139.35790.8336-0.03121.4087-0.5727-1.34940.7218-0.2766-0.28670.51580.35490.37160.16210.11260.15050.062833.85454.98454.637
92.02161.69020.751612.27716.38293.5980.1884-0.20740.2162-0.45190.0806-0.1049-0.86510.1111-0.2690.2091-0.01690.2747-0.08110.05540.063649.73249.12451.466
103.2673-1.9228-4.12594.9716-0.685211.31410.50490.32010.1978-0.5372-0.3649-0.1994-0.8942-0.3258-0.14-0.02430.0880.0251-0.12390.0221-0.168940.11443.12654.598
110.3405-0.12820.28580.94130.61792.65520.00220.001-0.14120.22850.0947-0.0760.47130.0853-0.0969-0.15740.01950.0077-0.1557-0.0018-0.140642.20919.27567.843
1228.982516.5144-6.12517.7077-4.36857.5011-0.4277-1.2257-0.4081.39560.56750.8039-0.2983-0.693-0.13980.19150.36550.21980.44110.14290.041832.06549.51327.701
133.1991-1.12112.8233.2945-0.445811.0697-0.254-0.25260.24780.32030.216-0.0539-0.5472-0.48930.038-0.1010.0876-0.0052-0.08790.0034-0.161338.70253.3812.952
142.23130.8660.68338.9784-4.39223.7614-0.0764-0.2864-0.46840.10860.34870.14420.1868-0.5942-0.2724-0.127-0.0145-0.00850.05080.0898-0.047334.10640.07114.561
151.86060.23851.53342.15532.29464.75780.16570.0091-0.34380.0890.0915-0.09170.857-0.2216-0.25730.0181-0.03920.0256-0.0552-0.02020.021943.21810.48135.622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 62
2X-RAY DIFFRACTION2A63 - 137
3X-RAY DIFFRACTION3B2 - 30
4X-RAY DIFFRACTION4B31 - 60
5X-RAY DIFFRACTION5B61 - 94
6X-RAY DIFFRACTION6B95 - 129
7X-RAY DIFFRACTION7B130 - 139
8X-RAY DIFFRACTION8C2 - 7
9X-RAY DIFFRACTION9C8 - 25
10X-RAY DIFFRACTION10C26 - 42
11X-RAY DIFFRACTION11C43 - 73
12X-RAY DIFFRACTION12D2 - 8
13X-RAY DIFFRACTION13D9 - 23
14X-RAY DIFFRACTION14D24 - 45
15X-RAY DIFFRACTION15D46 - 73

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