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- PDB-3otv: Crystal structure of the intracellular domain of Rv3910 from Myco... -

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Basic information

Entry
Database: PDB / ID: 3otv
TitleCrystal structure of the intracellular domain of Rv3910 from Mycobacterium tuberculosis
ComponentsPROBABLE CONSERVED TRANSMEMBRANE PROTEIN
KeywordsTRANSFERASE / peptidoglycan / Ser/Thr kinase / pseudokinase / Regulation / Membrane
Function / homology
Function and homology information


lipid-linked peptidoglycan transport / lipid-linked peptidoglycan transporter activity / lipid translocation / membrane => GO:0016020 / peptidoglycan biosynthetic process / regulation of cell shape / extracellular region / plasma membrane
Similarity search - Function
Peptidoglycan biosynthesis protein MurJ / : / Lipid II flippase MurJ / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle ...Peptidoglycan biosynthesis protein MurJ / : / Lipid II flippase MurJ / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / MOLECULAR REPLACEMENT / Resolution: 3.094 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 14, 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 1.2Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
B: PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
C: PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
D: PROBABLE CONSERVED TRANSMEMBRANE PROTEIN


Theoretical massNumber of molelcules
Total (without water)120,5364
Polymers120,5364
Non-polymers00
Water1,08160
1
A: PROBABLE CONSERVED TRANSMEMBRANE PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,1341
Polymers30,1341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROBABLE CONSERVED TRANSMEMBRANE PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,1341
Polymers30,1341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROBABLE CONSERVED TRANSMEMBRANE PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,1341
Polymers30,1341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PROBABLE CONSERVED TRANSMEMBRANE PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,1341
Polymers30,1341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.037, 59.687, 145.063
Angle α, β, γ (deg.)90.00, 97.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROBABLE CONSERVED TRANSMEMBRANE PROTEIN


Mass: 30133.941 Da / Num. of mol.: 4 / Fragment: Intracellular domain, 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.: 60 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.7-0.8M succinate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2007 / Details: Double flat crystal, Si(111)
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 3.094→40.814 Å / Num. all: 18293 / Num. obs: 15986 / % possible obs: 87.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 53.43 Å2 / Rmerge(I) obs: 0.631 / Rsym value: 0.113 / Net I/σ(I): 9.9
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.73 / Num. unique all: 1290 / Rsym value: 0.39 / % possible all: 70.8

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Processing

Software
NameVersionClassification
ELVESrefinement
PHENIX- Phasermodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX- Phaserphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OUK

3ouk


Resolution: 3.094→40.814 Å / SU ML: 0.43 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: ML / Details: Phenix
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 827 5.18 %Random
Rwork0.1893 ---
all0.1924 15972 --
obs0.1924 15972 87.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.537 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 60.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.0543 Å20 Å2-8.801 Å2
2---2.9602 Å2-0 Å2
3---7.0145 Å2
Refine analyzeLuzzati coordinate error obs: 0.512 Å
Refinement stepCycle: LAST / Resolution: 3.094→40.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7453 0 0 60 7513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017589
X-RAY DIFFRACTIONf_angle_d1.30310375
X-RAY DIFFRACTIONf_dihedral_angle_d12.7612781
X-RAY DIFFRACTIONf_chiral_restr0.0761223
X-RAY DIFFRACTIONf_plane_restr0.0061391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.0941-3.28790.27671170.24032094209573
3.2879-3.54160.31661320.2212382239183
3.5416-3.89770.3669900.25381928192967
3.8977-4.46120.20941630.166628782878100
4.4612-5.61830.24281560.164428902890100
5.6183-40.81760.21081690.173829732974100

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