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- PDB-5imu: A fragment of conserved hypothetical protein Rv3899c (residues 18... -

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Basic information

Entry
Database: PDB / ID: 5imu
TitleA fragment of conserved hypothetical protein Rv3899c (residues 184-410) from Mycobacterium tuberculosis
ComponentsTat (Twin-arginine translocation) pathway signal sequence containing protein
KeywordsSIGNALING PROTEIN / alpha/beta/alpha sandwich / alpha helix bundule
Function / homologyDomain of unknown function DUF5632 / Protein of unknown function DUF5631 / Family of unknown function (DUF5631) / Family of unknown function (DUF5632) / extracellular region / : / Tat (Twin-arginine translocation) pathway signal sequence containing protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.9 Å
AuthorsLi, D.F. / Gao, Y.R. / Liu, Y.Y. / Bi, L.J.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystal structure of Rv3899c(184-410), a hypothetical protein from Mycobacterium tuberculosis
Authors: Liu, Y.Y. / Gao, Y.R. / Li, D.F. / Fleming, J. / Li, H.L. / Bi, L.J.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tat (Twin-arginine translocation) pathway signal sequence containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2912
Polymers24,2511
Non-polymers391
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50 Å2
ΔGint-0 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.155, 54.973, 75.807
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 Tat (Twin-arginine translocation) pathway signal sequence containing protein / Conserved hypothetical protein Rv3899c / Uncharacterized protein


Mass: 24251.449 Da / Num. of mol.: 1 / Fragment: UNP residues 184-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3899c, LH57_21230 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O05446
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium acetate, 0.1M bis-tris (pH 5.5), 25% PEG 3350
PH range: 5.0-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→44.51 Å / Num. obs: 16973 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.5 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→44.503 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19
RfactorNum. reflection% reflection
Rfree0.1895 850 5.02 %
Rwork0.1595 --
obs0.1611 16928 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 1 348 1995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031677
X-RAY DIFFRACTIONf_angle_d0.6162294
X-RAY DIFFRACTIONf_dihedral_angle_d11.5561019
X-RAY DIFFRACTIONf_chiral_restr0.04272
X-RAY DIFFRACTIONf_plane_restr0.004301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.01910.26481350.22412493X-RAY DIFFRACTION95
2.0191-2.1750.21171510.1762649X-RAY DIFFRACTION100
2.175-2.39380.23451230.15972696X-RAY DIFFRACTION100
2.3938-2.74020.20541400.16922690X-RAY DIFFRACTION100
2.7402-3.45210.17941270.15452736X-RAY DIFFRACTION100
3.4521-44.51530.15681740.14042814X-RAY DIFFRACTION100

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