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- PDB-3oun: Crystal structure of the FhaA FHA domain complexed with the intra... -

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Basic information

Entry
Database: PDB / ID: 3oun
TitleCrystal structure of the FhaA FHA domain complexed with the intracellular domain of Rv3910
Components
  • PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
  • Putative uncharacterized protein TB39.8
KeywordsPROTEIN BINDING/TRANSFERASE / peptidoglycan / Ser/Thr kinase / pseudokinase / FHA domain / regulation / phosphorylation / membrane associated intracellular / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


lipid-linked peptidoglycan transport / lipid-linked peptidoglycan transporter activity / lipid translocation / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape / membrane => GO:0016020 / mRNA binding / extracellular region / plasma membrane / cytosol
Similarity search - Function
FhaA, N-terminal domain / FhaA, N-terminal domain superfamily / FhaA, N-terminal domain / Peptidoglycan biosynthesis protein MurJ / Lipid II flippase MurJ / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain ...FhaA, N-terminal domain / FhaA, N-terminal domain superfamily / FhaA, N-terminal domain / Peptidoglycan biosynthesis protein MurJ / Lipid II flippase MurJ / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Probable peptidoglycan biosynthesis protein MviN / FHA domain-containing protein FhaA / Probable peptidoglycan biosynthesis protein MviN
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.705 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 1.2Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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 TB39.8
B: PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2243
Polymers47,1692
Non-polymers551
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-7 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.709, 80.709, 139.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-283-

MN

21B-316-

HOH

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Components

#1: Protein Putative uncharacterized protein TB39.8


Mass: 16687.986 Da / Num. of mol.: 1 / Fragment: UNP residues 390-524
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0020c, TB39.8 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus / References: UniProt: P71590
#2: Protein PROBABLE CONSERVED TRANSMEMBRANE PROTEIN


Mass: 30481.244 Da / Num. of mol.: 1 / Fragment: UNP residues 676-963
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
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M CaCl2, 0.1M MES pH 6, 1mM MnCl2, 20% PEG 6000, 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: Apr 10, 2009 / Details: DCM
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 14950 / Num. obs: 14926 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 36.8 Å2 / Rsym value: 0.23 / Net I/σ(I): 6.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.77 / Num. unique all: 1467 / Rsym value: 0.904 / % possible all: 99.2

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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 ENTRIES 3OTV and 2FEZ

3otv

2fez


Resolution: 2.705→49.431 Å / SU ML: 0.35 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 735 4.94 %Random
Rwork0.1838 ---
all0.1866 14950 --
obs0.1866 14885 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.856 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0094 Å2-0 Å20 Å2
2--0.0094 Å2-0 Å2
3----0.0189 Å2
Refinement stepCycle: LAST / Resolution: 2.705→49.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2624 0 1 177 2802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082691
X-RAY DIFFRACTIONf_angle_d1.1143676
X-RAY DIFFRACTIONf_dihedral_angle_d16.095998
X-RAY DIFFRACTIONf_chiral_restr0.072426
X-RAY DIFFRACTIONf_plane_restr0.005495
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.705-2.91390.31251600.2404274699
2.9139-3.20710.24561370.19392789100
3.2071-3.6710.221500.15732814100
3.671-4.62460.19911450.132824100
4.6246-49.43890.20861430.17922977100

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