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- PDB-4tmd: X-ray structure of Putative uncharacterized protein (Rv0999 ortho... -

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Basic information

Entry
Database: PDB / ID: 4tmd
TitleX-ray structure of Putative uncharacterized protein (Rv0999 ortholog) from Mycobacterium smegmatis
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyDomain of unknown function DUF5642 / Domain of unknown function (DUF5642) / IODIDE ION / DUF5642 domain-containing protein
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsHoranyi, P.S. / Dranow, D.M. / Abendroth, J. / Lorimer, D. / Edwards, T. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: X-ray structure of Putative uncharacterized protein (Rv0999 ortholog) from Mycobacterium smegmatis
Authors: Horanyi, P.S. / Dranow, D.M. / Abendroth, J. / Lorimer, D. / Edwards, T.
History
DepositionJun 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5947
Polymers20,8331
Non-polymers7616
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.980, 37.830, 151.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

21A-466-

HOH

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Components

#1: Protein Uncharacterized protein / Rv0999 ortholog


Mass: 20832.590 Da / Num. of mol.: 1 / Fragment: UNP residues 31-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5452 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R3F3
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 24 % w/v PEG 1500/ 20 % v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNumber: 695979 / Rmerge(I) obs: 0.053 / Χ2: 1.03 / D res high: 2 Å / Num. obs: 24800 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
6.328.9449710.025
5.166.3267410.029
4.475.1678210.028
44.4788510.03
3.65496010.035
3.383.65106410.036
3.163.38113810.042
2.983.16120910.052
2.832.98130410.063
2.72.83133910.08
2.582.7141310.088
2.482.58148110.113
2.392.48148410.127
2.312.39161010.147
2.242.31163610.157
2.172.24169010.179
2.112.17170910.211
2.052.11182010.238
22.05181510.296
ReflectionResolution: 2→37.91 Å / Num. obs: 24800 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 28.06 % / Rmerge F obs: 1 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.054 / Χ2: 1.035 / Net I/σ(I): 56.03 / Num. measured all: 695979
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.050.9810.29610.5227487181718150.30699.9
2.05-2.110.9910.23815.0736092182018200.244100
2.11-2.170.9950.21120.1344910170917090.215100
2.17-2.240.9970.17924.5250221169016900.182100
2.24-2.310.9980.15727.548811163616360.16100
2.31-2.390.9980.14729.5648397161016100.149100
2.39-2.480.9980.12733.344589148414840.129100
2.48-2.580.9990.11336.8144758148114810.115100
2.58-2.70.9990.08845.2542949141314130.089100
2.7-2.830.9990.0850.5440810133913390.081100
2.83-2.9810.06361.4639933130413040.064100
2.98-3.1610.05272.136985120912090.053100
3.16-3.3810.04291.6134950113811380.043100
3.38-3.6510.036109.832655106410640.036100
3.65-410.035120.98292829609600.035100
4-4.4710.03137.94269478858850.03100
4.47-5.1610.028140.68237937827820.028100
5.16-6.3210.029133.35200976746740.03100
6.32-8.9410.025140.09144194984970.02599.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
SHELXphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→37.907 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 20.61 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2159 1234 4.98 %
Rwork0.188 23529 -
obs0.1894 24763 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.57 Å2 / Biso mean: 30.4841 Å2 / Biso min: 10.13 Å2
Refinement stepCycle: final / Resolution: 2→37.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 6 129 1548
Biso mean--106.22 35.79 -
Num. residues----190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081447
X-RAY DIFFRACTIONf_angle_d1.1511968
X-RAY DIFFRACTIONf_chiral_restr0.048224
X-RAY DIFFRACTIONf_plane_restr0.005266
X-RAY DIFFRACTIONf_dihedral_angle_d14.314540
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.08020.24591380.204726202758
2.0802-2.17480.20741430.20426162759
2.1748-2.28950.25391320.198425962728
2.2895-2.43290.30981340.208725932727
2.4329-2.62070.23831340.200826312765
2.6207-2.88430.22181290.198826192748
2.8843-3.30150.23271330.19626612794
3.3015-4.15870.18211390.169925952734
4.1587-37.91430.18541520.173325982750

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