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- PDB-4n8o: Crystal structure of Mycobacterial FtsX extracellular domain, bro... -

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Basic information

Entry
Database: PDB / ID: 4n8o
TitleCrystal structure of Mycobacterial FtsX extracellular domain, bromide derivative
ComponentsCell division protein FtsX
KeywordsMEMBRANE PROTEIN / Cell wall
Function / homology
Function and homology information


peptidoglycan-based cell wall / cell cycle / cell division / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #3040 / : / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / ABC3 transporter permease protein domain / FtsX-like permease family / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / : / Cell division protein FtsX
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsMavrici, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Mycobacterium tuberculosis FtsX extracellular domain activates the peptidoglycan hydrolase, RipC.
Authors: Mavrici, D. / Marakalala, M.J. / Holton, J.M. / Prigozhin, D.M. / Gee, C.L. / Zhang, Y.J. / Rubin, E.J. / Alber, T.
History
DepositionOct 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein FtsX
B: Cell division protein FtsX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,40510
Polymers25,9292
Non-polymers4768
Water2,828157
1
A: Cell division protein FtsX
hetero molecules

B: Cell division protein FtsX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,40510
Polymers25,9292
Non-polymers4768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-y+1,x+1,z1
Buried area1150 Å2
ΔGint-11 kcal/mol
Surface area11590 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-8 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.167, 133.167, 28.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Cell division protein FtsX / Signalling protein A


Mass: 12964.396 Da / Num. of mol.: 2 / Fragment: UNP residues 45-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ftsX, MT3185, MTCY164.12c, Rv3101c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WG19
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 291 K / pH: 8
Details: 25% PEG MME 2000, 150mM KBr, pH 8, 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: 0.92004 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2013
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92004 Å / Relative weight: 1
ReflectionRedundancy: 13.8 % / Number: 256255 / Rmerge(I) obs: 0.371 / Χ2: 1.05 / D res high: 1.99 Å / Num. obs: 33526 / % possible obs: 99.2
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
8.915038199.50.0321.22914
6.38.916831000.0651.07814.3
5.146.38921000.0940.99813.8
4.455.1410791000.0711.05114.3
3.984.4511761000.0761.06414.2
3.643.9813281000.1051.07714.1
3.373.6414511000.1341.0613.9
3.153.3715341000.2051.01913.7
2.973.1516531000.2791.00313.6
2.822.9717571000.41.00213.4
2.692.8218331000.5510.9913.4
2.572.6919081000.7751.00713.2
2.472.5720221000.948
2.382.4720511001.12
2.32.3821951001.211
2.232.321731001.503
2.162.2323071001.723
2.12.1624021002.165
2.042.123911002.487
1.992.04231090.23.255
ReflectionResolution: 2.3→50 Å / Num. all: 21912 / Num. obs: 21912

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→47.08 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.23 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1106 5.05 %
Rwork0.191 --
obs0.193 21912 99.9 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1560 0 8 157 1725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081586
X-RAY DIFFRACTIONf_angle_d0.8882134
X-RAY DIFFRACTIONf_dihedral_angle_d13.298600
X-RAY DIFFRACTIONf_chiral_restr0.071238
X-RAY DIFFRACTIONf_plane_restr0.004286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3024-2.40710.29851460.26032650X-RAY DIFFRACTION99
2.4071-2.53410.28481340.26162541X-RAY DIFFRACTION100
2.5341-2.69280.30691410.22862606X-RAY DIFFRACTION100
2.6928-2.90070.25051410.21282629X-RAY DIFFRACTION100
2.9007-3.19250.22911440.20032589X-RAY DIFFRACTION100
3.1925-3.65440.22391420.16642580X-RAY DIFFRACTION100
3.6544-4.60350.19641320.15162591X-RAY DIFFRACTION100
4.6035-47.09150.22571260.17132620X-RAY DIFFRACTION100

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