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- PDB-3ol3: Crystal structure of a putative uncharacterized protein from Myco... -

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Basic information

Entry
Database: PDB / ID: 3ol3
TitleCrystal structure of a putative uncharacterized protein from Mycobacterium smegamtis, an ortholog of Rv0543c, iodide phased
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / Mycobacterium / tuberculosis / Rv0543c / ortholog / iodide ion SAD phasing / 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
IODIDE ION / TRIETHYLENE GLYCOL / EndoIII-related endonuclease
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.95 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 1.4Feb 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: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,55026
Polymers23,3902
Non-polymers3,16024
Water2,774154
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-3 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.870, 72.900, 45.140
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: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 52.57 mg/mL MysmA.17112.a.A1 PS00688 in 25 mM Hepes pH 7.5, 0.5 M NaCl, 5% glycerol grown against JCSG+ screen conditions D2, 0.2 M MgCl2, 0.1 M Na Hepes pH 7.5, 30% PEG 400 and soaked ...Details: 52.57 mg/mL MysmA.17112.a.A1 PS00688 in 25 mM Hepes pH 7.5, 0.5 M NaCl, 5% glycerol grown against JCSG+ screen conditions D2, 0.2 M MgCl2, 0.1 M Na Hepes pH 7.5, 30% PEG 400 and soaked against 1.0 M NaI, 0.2 M MgCl2, 0.1 M Na Hepes pH 7.0, 35% PEG 400 for 5 minutes, crystal tracking ID 217009d2, VAPOR DIFFUSION, SITTING DROP

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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 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 214563 / Rmerge(I) obs: 0.068 / D res high: 1.95 Å / Num. obs: 32341 / % possible obs: 96.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1.952219888.810.504
22.06219791.710.393
2.062.1222419510.35
2.122.18218096.410.27
2.182.25214996.710.208
2.252.33204197.110.185
2.332.42202197.410.168
2.422.52194097.610.153
2.522.63186798.310.127
2.632.76177898.410.103
2.762.91168898.310.084
2.913.0816089910.069
3.083.3155699.110.051
3.33.56139499.210.04
3.563.9131399.510.032
3.94.36116399.710.029
4.365.04107399.810.029
5.046.1788299.910.034
6.178.7267410010.028
ReflectionResolution: 1.95→50 Å / Num. all: 17898 / Num. obs: 17265 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 27.164 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 21.83
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.95-20.537493631149188.5
2-2.060.425.2101581149191.2
2.06-2.120.3736.4112781169194.6
2.12-2.180.2888.4118291145196
2.18-2.250.22410.7123151126196.2
2.25-2.330.19912.4125231074196.6
2.33-2.420.18213.9133681063196.9
2.42-2.520.16616.6147741026197
2.52-2.630.1419.314399986197.8
2.63-2.760.1192213762943198
2.76-2.910.0982513091898197.7
2.91-3.080.08328.512471860198.5
3.08-3.30.06334.512020837198.8
3.3-3.560.05341.610800751198.8
3.56-3.90.04745.810119714199.2
3.9-4.360.04449.58964637199.4
4.36-5.040.04847.68250599199.7
5.04-6.170.06243.96684499199.8
6.17-8.720.05746.749623941100

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.95 Å / D res low: 45.14 Å / FOM : 0.433 / FOM acentric: 0.464 / FOM centric: 0.215 / Reflection: 17200 / Reflection acentric: 15076 / Reflection centric: 2109
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.92-11.040.3310.4170.16218912564
6.5-7.920.4380.5090.26323116467
5.65-6.50.4810.5430.30126619868
5.06-5.650.4670.5230.26630523867
4.62-5.060.4210.4990.13133926772
4.28-4.620.4510.5160.15234528461
4.01-4.280.4560.5250.1538431371
3.78-4.010.4760.5430.12439633363
3.59-3.780.4950.5590.16142335568
3.42-3.590.5160.5760.15543137060
3.28-3.420.5180.5680.2346439668
3.15-3.280.4790.5290.17547540966
3.03-3.150.4820.5230.19548442459
2.93-3.030.4860.530.21751744572
2.84-2.930.4870.520.22951145457
2.76-2.840.4960.5330.22654247666
2.68-2.760.5140.5460.2454648858
2.61-2.680.480.5160.256950366
2.54-2.610.4860.5140.24757651462
2.48-2.540.470.4980.22458752760
2.42-2.480.4870.5120.2560054258
2.37-2.420.4630.4880.22960654660
2.32-2.370.4340.4580.19662156457
2.27-2.320.440.4580.27164158061
2.23-2.270.4060.4290.19564658264
2.19-2.230.3810.3950.22565459657
2.15-2.190.3750.3870.25465860058
2.11-2.150.3780.3950.20470463864
2.08-2.110.3390.350.20767061454
2.04-2.080.3360.3450.23967061455
2.01-2.040.3440.350.26769463953
1.98-2.010.3550.3640.25267161752
1.95-1.980.3320.3370.27766060453

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASEREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2147 / WRfactor Rwork: 0.1853 / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.849 / SU B: 6.411 / SU ML: 0.097 / SU R Cruickshank DPI: 0.1659 / SU Rfree: 0.1525 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 876 5.1 %RANDOM
Rwork0.1966 ---
obs0.1985 17200 96.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.13 Å2 / Biso mean: 25.2377 Å2 / Biso min: 11.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 54 154 1666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221543
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9792101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3585196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49624.62767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73315242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4021510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211158
X-RAY DIFFRACTIONr_mcbond_it0.7951.5963
X-RAY DIFFRACTIONr_mcangle_it1.40821557
X-RAY DIFFRACTIONr_scbond_it2.1583580
X-RAY DIFFRACTIONr_scangle_it3.4844.5540
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 65 -
Rwork0.226 1079 -
all-1144 -
obs--88.27 %
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)
13.1959-0.8666-0.40630.53290.20310.02290.06710.1198-0.09370.0004-0.07430.0507-0.0128-0.0130.00710.04050.01350.00250.0696-0.0110.004638.58315.571233.0994
20.2294-0.65930.16012.5403-0.27290.110.00320.03470.0140.0511-0.0173-0.06230.00620.01510.01410.04990.01690.00260.04750.00350.021856.636433.860436.0031
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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