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- PDB-3h6p: Crystal structure of Rv3019c-Rv3020c from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3h6p
TitleCrystal structure of Rv3019c-Rv3020c from Mycobacterium tuberculosis
Components
  • ESAT-6 LIKE PROTEIN ESXS
  • ESAT-6-like protein esxR
Keywordsstructural genomics / unknown function / Four-helix bundle / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC / Integrated Center for Structure and Function Innovation / ISFI
Function / homology
Function and homology information


protein-containing complex / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #190 / ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / ESAT-6-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ESAT-6-like protein EsxR / ESAT-6-like protein EsxR / ESAT-6-like protein EsxS
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsChan, S. / Arbing, M. / Phan, T. / Kaufmann, M. / Cascio, D. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) / Integrated Center for Structure and Function Innovation (ISFI)
CitationJournal: To be Published
Title: Crystal structure of Rv3019c-Rv3020c from Mycobacterium tuberculosis
Authors: Chan, S. / Arbing, M. / Phan, T. / Kaufmann, M. / Cascio, D. / Eisenberg, D.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESAT-6 LIKE PROTEIN ESXS
B: ESAT-6 LIKE PROTEIN ESXS
C: ESAT-6-like protein esxR
D: ESAT-6-like protein esxR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8685
Polymers43,7764
Non-polymers921
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-76 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.288, 54.572, 103.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ESAT-6 LIKE PROTEIN ESXS


Mass: 11570.802 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: esxS, Rv3019c, Rv3020c / Plasmid: pET46EkLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q6MX18
#2: Protein ESAT-6-like protein esxR


Mass: 10317.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: esxR, MT3104, MTV012.33c, Rv3019c, Rv3020c / Plasmid: pET46-EkLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P64093, UniProt: P9WNI9*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 26% PEG1500, 0.1 M MMT pH 7.0, , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97849 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2009
RadiationMonochromator: Cryo-Cooled Si(111) double crystal. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 1.91→80 Å / Num. all: 18085 / Num. obs: 18085 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rsym value: 0.073 / Net I/σ(I): 25.5
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 6.1 / Rsym value: 0.472 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.4.0061refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.91→51.57 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.463 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 957 5.3 %RANDOM
Rwork0.19603 ---
all0.19814 18226 --
obs0.19822 17080 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.911 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2--1.45 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.91→51.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1753 0 6 142 1901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211811
X-RAY DIFFRACTIONr_bond_other_d0.0010.021127
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.8922456
X-RAY DIFFRACTIONr_angle_other_deg0.87732751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1925242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.94225.61889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34415268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.701156
X-RAY DIFFRACTIONr_chiral_restr0.0640.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7021.51175
X-RAY DIFFRACTIONr_mcbond_other0.1691.5499
X-RAY DIFFRACTIONr_mcangle_it1.35721823
X-RAY DIFFRACTIONr_scbond_it2.4423636
X-RAY DIFFRACTIONr_scangle_it3.8484.5629
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.912→1.962 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 66 -
Rwork0.212 1196 -
obs--96.7 %
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)
17.60550.89-4.79440.1346-0.50433.12820.00030.29270.09480.00370.03570.0087-0.0015-0.2-0.0360.02520.00320.00570.04890.03810.0124-14.50232.7348-23.3777
27.07270.9488-4.74370.3697-0.76413.58620.05150.00460.08330.0123-0.01930.0132-0.08390.0434-0.03220.0749-0.0073-0.01120.05460.0060.0415-12.75881.3128-12.8003
32.73820.595-1.1632.1612-0.6981.97550.1912-0.24250.16520.2224-0.10450.0534-0.23480.1055-0.08670.0809-0.0275-0.020.0034-0.01330.0656-37.1356.74553.1164
42.51632.1038-1.34332.7664-1.78543.60420.0658-0.0250.20650.0405-0.02960.0774-0.202-0.07-0.03620.04170.03040.0073-0.0091-0.0010.08689.695813.7336-36.017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 76
2X-RAY DIFFRACTION2B14 - 80
3X-RAY DIFFRACTION3C20 - 75
4X-RAY DIFFRACTION4D20 - 74

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