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- PDB-4n8n: Crystal structure of Mycobacterial FtsX extracellular domain -

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Basic information

Entry
Database: PDB / ID: 4n8n
TitleCrystal structure of Mycobacterial FtsX extracellular domain
ComponentsCell division protein FtsX
KeywordsMEMBRANE PROTEIN / Cell wall
Function / homology
Function and homology information


peptidoglycan-based cell wall / 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 C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Cell division protein FtsX
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.874 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
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,9366
Polymers51,8584
Non-polymers782
Water8,593477
1
A: Cell division protein FtsX


Theoretical massNumber of molelcules
Total (without water)12,9641
Polymers12,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division protein FtsX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0032
Polymers12,9641
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cell division protein FtsX


Theoretical massNumber of molelcules
Total (without water)12,9641
Polymers12,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cell division protein FtsX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0032
Polymers12,9641
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.248, 150.009, 28.658
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Cell division protein FtsX


Mass: 12964.396 Da / Num. of mol.: 4 / 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / 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: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2012
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 38850 / Num. obs: 38783 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.77 Å2 / Rmerge(I) obs: 0.111 / Χ2: 0.964 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.87-1.946.40.83936530.985195.3
1.94-2.016.80.59738141.0451100
2.01-2.116.90.40338211.0281100
2.11-2.226.90.29938781.0291100
2.22-2.3670.22638451.0961100
2.36-2.5470.1838491.0161100
2.54-2.7970.1338880.951100
2.79-3.26.90.09239420.8111100
3.2-4.036.90.08639590.8861100
4.03-506.50.04742010.801199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.874→45.243 Å / Occupancy max: 1 / Occupancy min: 0.82 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 2000 5.16 %
Rwork0.1862 --
obs0.1886 38773 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.63 Å2 / Biso mean: 27.373 Å2 / Biso min: 4.37 Å2
Refinement stepCycle: LAST / Resolution: 1.874→45.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3186 0 2 477 3665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073239
X-RAY DIFFRACTIONf_angle_d0.984358
X-RAY DIFFRACTIONf_chiral_restr0.041485
X-RAY DIFFRACTIONf_plane_restr0.004584
X-RAY DIFFRACTIONf_dihedral_angle_d14.0581228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.874-1.92090.3181360.26262498263495
1.9209-1.97280.28531380.240525392677100
1.9728-2.03090.27071430.209326152758100
2.0309-2.09640.22661380.197225512689100
2.0964-2.17140.23021420.189126112753100
2.1714-2.25830.21251410.187625852726100
2.2583-2.36110.26231430.187226402783100
2.3611-2.48560.27241400.207925642704100
2.4856-2.64130.22631440.201426572801100
2.6413-2.84520.24291430.192926312774100
2.8452-3.13140.22491440.180226442788100
3.1314-3.58440.21721460.168126862832100
3.5844-4.51530.20691460.15826752821100
4.5153-45.25620.23071560.187728773033100

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