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- PDB-3uid: Crystal Structure of Protein Ms6760 from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 3uid
TitleCrystal Structure of Protein Ms6760 from Mycobacterium smegmatis
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / uncharacterized protein / SRPBCC superfamily / beta sandwich / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Activator of Hsp90 ATPase homologue 1/2-like C-terminal domain-containing protein
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.571 Å
AuthorsBajaj, R.A. / Miallau, L. / Cascio, D. / Arbing, M. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystal structure of the toxin Msmeg_6760, the structural homolog of Mycobacterium tuberculosis Rv2035, a novel type II toxin involved in the hypoxic response.
Authors: Bajaj, R.A. / Arbing, M.A. / Shin, A. / Cascio, D. / Miallau, L.
History
DepositionNov 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)37,1352
Polymers37,1352
Non-polymers00
Water3,549197
1
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,5671
Polymers18,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,5671
Polymers18,5671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.320, 60.210, 100.980
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 Putative uncharacterized protein


Mass: 18567.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2-155 / Gene: MSMEG_6760 / Plasmid: pMAPLe3 (pET 28 derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0R731
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 1.98 Å3/Da / Density % sol: 37.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M Na Acetate pH 4.5, 20% PEG 3000, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.57→19.63 Å / Num. obs: 39602 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 22.699 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.57-1.610.5172.034757208268.7
1.61-1.660.4352.657377267390.5
1.66-1.710.3663.358280277496.2
1.71-1.760.2924.178443272096.9
1.76-1.820.2225.368333263496.7
1.82-1.880.1657.258330256597.4
1.88-1.950.1319.088372250198.1
1.95-2.030.09312.788354242297.9
2.03-2.120.07315.948055229998.1
2.12-2.220.06218.727879221298
2.22-2.340.05720.657604211298.2
2.34-2.490.05122.457284201698.1
2.49-2.660.04524.686788187698.1
2.66-2.870.03729.076335177998.1
2.87-3.150.03332.595799162198.5
3.15-3.520.02637.425232149198.2
3.52-4.060.02540.294606132197.3
4.06-4.970.02142.713876111597.9
4.97-7.030.02141.59319190698.2
7.030.01942.2160748389.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XUV

1xuv


Resolution: 1.571→19.627 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8723 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 19.86 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3965 10 %RANDOM
Rwork0.1917 ---
obs0.1939 -94.9 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.002 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 88.16 Å2 / Biso mean: 17.7685 Å2 / Biso min: 4.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.8706 Å20 Å20 Å2
2---0.5151 Å20 Å2
3---1.3858 Å2
Refinement stepCycle: LAST / Resolution: 1.571→19.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 0 197 2675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062620
X-RAY DIFFRACTIONf_angle_d1.0433607
X-RAY DIFFRACTIONf_chiral_restr0.075403
X-RAY DIFFRACTIONf_plane_restr0.005474
X-RAY DIFFRACTIONf_dihedral_angle_d11.925921
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.571-1.59050.2857860.250577586159
1.5905-1.61070.2481150.22751030114577
1.6107-1.63190.32341240.2391114123885
1.6319-1.65420.25861380.21791241137994
1.6542-1.67780.2761410.2111271141296
1.6778-1.70280.2341410.22181273141497
1.7028-1.72940.27291460.20991314146097
1.7294-1.75780.24671390.20841250138996
1.7578-1.78810.23011440.20481289143397
1.7881-1.82060.22641390.18781258139796
1.8206-1.85550.1991460.18121311145798
1.8555-1.89340.241440.19151299144397
1.8934-1.93450.22091470.19941326147398
1.9345-1.97950.22961430.18791287143098
1.9795-2.02890.21451470.18841319146697
2.0289-2.08370.21681440.17851298144298
2.0837-2.1450.20461460.19391318146498
2.145-2.21410.19711450.18551299144498
2.2141-2.29320.23171460.18341317146398
2.2932-2.38480.20851460.1881312145898
2.3848-2.49310.21311480.19461336148498
2.4931-2.62430.20651450.20241305145098
2.6243-2.78830.24641480.19921334148299
2.7883-3.00290.25061500.2241341149198
3.0029-3.30380.20691470.20381327147498
3.3038-3.77890.17691510.18541357150898
3.7789-4.74980.15291510.15111361151297
4.7498-19.6290.20191580.18051430158897
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)
10.4936-0.0214-0.23731.05040.20871.133-0.0469-0.0031-0.0257-0.02120.0413-0.0216-0.00790.04820.01940.0297-0.0067-0.00570.0511-0.00510.0551-1.50295.0374-6.7276
21.1055-0.0420.5631.22350.35251.3597-0.045-0.1795-0.0860.11020.06530.1349-0.012-0.1478-0.00470.08970.01820.0040.08630.03150.07513.2994-7.295515.0533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 164
2X-RAY DIFFRACTION2chain BB2 - 163

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