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- PDB-3ol4: Crystal structure of a putative uncharacterized protein from Myco... -

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Basic information

Entry
Database: PDB / ID: 3ol4
TitleCrystal structure of a putative uncharacterized protein from Mycobacterium smegmatis, an ortholog of Rv0543c
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / mycobacterium tuberculosis / ortholog / Rv0543c / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


Arc Repressor Mutant, subunit A - #2390 / Helix Hairpins - #2080 / Protein of unknown function DUF3349 / Protein of unknown function (DUF3349) / Helix Hairpins / Helix non-globular / Special / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
EndoIII-related endonuclease
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: Protein Sci. / Year: 2020
Title: Structural diversity in the Mycobacteria DUF3349 superfamily.
Authors: Buchko, G.W. / Abendroth, J. / Robinson, J.I. / Phan, I.Q. / Myler, P.J. / Edwards, T.E.
#1: Journal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionAug 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Feb 26, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)23,3902
Polymers23,3902
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-17 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.210, 72.690, 45.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsAUTHORS STATE THAT THE BIOLOGICAL MOLECULE IS UNKNOWN.

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Components

#1: Protein Putative uncharacterized protein


Mass: 11695.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_1066 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QRC4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 52.57 mg/mL MysmA,17112.a.A1 PS00688 against PACT screen condition F12, 0.2 M sodium malonate, 0.1 M BisTris Propane pH 6.5, 20% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal ...Details: 52.57 mg/mL MysmA,17112.a.A1 PS00688 against PACT screen condition F12, 0.2 M sodium malonate, 0.1 M BisTris Propane pH 6.5, 20% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 217010f12, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 11, 2010 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 16421 / Num. obs: 16088 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 29.089 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.25
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.050.2853.320801041186.5
2.05-2.110.2394.325961097196.1
2.11-2.170.2116.134591118198.3
2.17-2.240.1677.936721074199.1
2.24-2.310.1359.736211067199.5
2.31-2.390.1210.335031030199.5
2.39-2.480.11810.434591006199.8
2.48-2.580.112.33246949199.5
2.58-2.70.07914.93171925199.5
2.7-2.830.07173071895199.9
2.83-2.980.05918.32870830199.9
2.98-3.160.04821.42752803199.5
3.16-3.380.03728.42643768199.9
3.38-3.650.02835.82387700199.6
3.65-40.02444.62223659199.4
4-4.470.02150.81980585197.7
4.47-5.160.02149.11743525198.9
5.16-6.320.02441.31518450198
6.32-8.940.01950.41169362196.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OL3

3ol3


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2061 / WRfactor Rwork: 0.1766 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8283 / SU B: 9.434 / SU ML: 0.118 / SU R Cruickshank DPI: 0.1828 / SU Rfree: 0.1644 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 803 5 %RANDOM
Rwork0.202 ---
obs0.204 16005 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.39 Å2 / Biso mean: 37.8828 Å2 / Biso min: 12.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1475 0 0 169 1644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221527
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9672087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2415195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22624.49369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56215252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4971511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211163
X-RAY DIFFRACTIONr_mcbond_it0.9081.5964
X-RAY DIFFRACTIONr_mcangle_it1.65821558
X-RAY DIFFRACTIONr_scbond_it2.3653563
X-RAY DIFFRACTIONr_scangle_it3.8724.5526
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 49 -
Rwork0.268 989 -
all-1038 -
obs--86.21 %
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)
12.8527-0.81720.02410.45310.10130.05960.01440.118-0.1620.0617-0.0220.07410.01310.02590.00760.12860.00130.00430.1342-0.02690.116737.872115.386932.7802
20.2084-0.58740.05873.3725-0.23170.0247-0.05720.0874-0.01140.13740.0824-0.0983-0.01160.0061-0.02520.11110.0121-0.02610.1224-0.01610.098756.324133.078835.6177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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