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- PDB-3ouk: Crystal structure of Rv3910 from Mycobacterium Tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3ouk
TitleCrystal structure of Rv3910 from Mycobacterium Tuberculosis
ComponentsPROBABLE CONSERVED TRANSMEMBRANE PROTEIN
KeywordsTRANSFERASE / peptidoglycan / Ser/Thr kinase / pseudokinase / Regulation / membrane protein
Function / homology
Function and homology information


lipid-linked peptidoglycan transport / lipid-linked peptidoglycan transporter activity / lipid translocation / peptidoglycan biosynthetic process / regulation of cell shape / membrane => GO:0016020 / extracellular region / plasma membrane
Similarity search - Function
Peptidoglycan biosynthesis protein MurJ / Lipid II flippase MurJ / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Probable peptidoglycan biosynthesis protein MviN / Probable peptidoglycan biosynthesis protein MviN
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.402 Å
AuthorsGee, C.L. / Alber, T.
CitationJournal: Sci.Signal. / Year: 2012
Title: A phosphorylated pseudokinase complex controls cell wall synthesis in mycobacteria
Authors: Gee, C.L. / Papavinasasundaram, K.G. / Blair, S.R. / Baer, C.E. / Falick, A.M. / King, D.S. / Griffin, J.E. / Venghatakrishnan, H. / Zukauskas, A. / Wei, J.R. / Dhiman, R.K. / Crick, D.C. / ...Authors: Gee, C.L. / Papavinasasundaram, K.G. / Blair, S.R. / Baer, C.E. / Falick, A.M. / King, D.S. / Griffin, J.E. / Venghatakrishnan, H. / Zukauskas, A. / Wei, J.R. / Dhiman, R.K. / Crick, D.C. / Rubin, E.J. / Sassetti, C.M. / Alber, T.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.2Mar 20, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROBABLE CONSERVED TRANSMEMBRANE PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,1341
Polymers30,1341
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.360, 122.360, 66.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PROBABLE CONSERVED TRANSMEMBRANE PROTEIN


Mass: 30133.941 Da / Num. of mol.: 1 / Fragment: Intracellular construct, UNP residues 679-963
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT4029, Rv3910 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus / References: UniProt: O05435, UniProt: P9WJK3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.874.39
2
Crystal grow
Temperature (K)Crystal-IDMethodDetailsPH range
2911vapor diffusion, hanging drop3M NaCl, 0.1M Tris-HCl, pH 7.5-8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K7.5-8.5
2912vapor diffusion, hanging drop60% tacsimate, 4% 1,1,1,3,3,3 hexafluoro-2-propanol , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.115872
SYNCHROTRONALS 8.3.120.979648
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDAug 24, 2007double crystal monochromater
ADSC QUANTUM 315r2CCDJan 19, 2008double crystal monochromater
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1S111SINGLE WAVELENGTHMx-ray1
2S111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.1158721
20.9796481
ReflectionResolution: 3.4→45.172 Å / Num. all: 8168 / Num. obs: 7693 / % possible obs: 94.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 55.8 Å2 / Rsym value: 0.103 / Net I/σ(I): 12
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2 / Num. unique all: 568 / Rsym value: 0.383 / % possible all: 71.8

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Processing

Software
NameVersionClassification
ELVESrefinement
SOLVEphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: phased from SeMet crystal

Resolution: 3.402→45.172 Å / SU ML: 0.4 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 352 4.59 %Random
Rwork0.1966 ---
all0.1984 8168 --
obs0.1984 7675 94.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 103.421 Å2 / ksol: 0.401 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-20.379 Å20 Å2-0 Å2
2--20.379 Å20 Å2
3----40.7579 Å2
Refinement stepCycle: LAST / Resolution: 3.402→45.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 0 4 1848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011878
X-RAY DIFFRACTIONf_angle_d1.332567
X-RAY DIFFRACTIONf_dihedral_angle_d13.733689
X-RAY DIFFRACTIONf_chiral_restr0.073301
X-RAY DIFFRACTIONf_plane_restr0.005345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4024-3.89450.27061010.2516213484
3.8945-4.90570.19841290.1747252298
4.9057-45.17630.24971220.19122667100

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