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- PDB-4u39: Crystal Structure of FtsZ:MciZ Complex from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 4u39
TitleCrystal Structure of FtsZ:MciZ Complex from Bacillus subtilis
Components
  • Cell division factor
  • Cell division protein FtsZ
KeywordsCELL CYCLE / FtsZ / MciZ / protein complex
Function / homology
Function and homology information


cell septum / division septum assembly / FtsZ-dependent cytokinesis / sporulation resulting in formation of a cellular spore / cell division site / protein polymerization / cell division / GTPase activity / GTP binding / identical protein binding / cytoplasm
Similarity search - Function
Cell division inhibitor MciZ / Mother cell inhibitor of FtsZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ, C-terminal domain ...Cell division inhibitor MciZ / Mother cell inhibitor of FtsZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Cell division inhibitor MciZ / Cell division protein FtsZ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.194 Å
AuthorsBisson-Filho, A.W. / Discola, K.F. / Castellen, P. / Blasios, V. / Martins, A. / Sforca, M.L. / Garcia, W. / Zeri, A.C. / Erickson, H.P. / Dessen, A. / Gueiros-Filho, F.J.
CitationJournal: To be Published
Title: Crystal Structure of FtsZ:MciZ Complex from Bacillus subtilis
Authors: Bisson-Filho, A.W. / Discola, K.F. / Castellen, P. / Blasios, V. / Martins, A. / Sforca, M.L. / Garcia, W. / Zeri, A.C. / Erickson, H.P. / Dessen, A. / Gueiros-Filho, F.J.
History
DepositionJul 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein FtsZ
B: Cell division protein FtsZ
C: Cell division protein FtsZ
D: Cell division protein FtsZ
E: Cell division protein FtsZ
F: Cell division protein FtsZ
G: Cell division protein FtsZ
H: Cell division protein FtsZ
I: Cell division protein FtsZ
J: Cell division factor
K: Cell division factor
L: Cell division factor
M: Cell division factor
N: Cell division factor
O: Cell division factor
P: Cell division factor
Q: Cell division factor
R: Cell division factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,42634
Polymers345,90618
Non-polymers1,52016
Water00
1
A: Cell division protein FtsZ
J: Cell division factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6244
Polymers38,4342
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division protein FtsZ
K: Cell division factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6244
Polymers38,4342
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cell division protein FtsZ
L: Cell division factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6244
Polymers38,4342
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cell division protein FtsZ
M: Cell division factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6244
Polymers38,4342
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cell division protein FtsZ
N: Cell division factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5293
Polymers38,4342
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cell division protein FtsZ
O: Cell division factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5293
Polymers38,4342
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Cell division protein FtsZ
P: Cell division factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6244
Polymers38,4342
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Cell division protein FtsZ
Q: Cell division factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6244
Polymers38,4342
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Cell division protein FtsZ
R: Cell division factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6244
Polymers38,4342
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.360, 167.360, 528.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Cell division protein FtsZ


Mass: 31476.879 Da / Num. of mol.: 9 / Fragment: UNP residues 12-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ftsZ, BSU15290 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17865
#2: Protein
Cell division factor / MciZ


Mass: 6957.148 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: mciZ, BSU23616 / Plasmid: pAB50 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L8EBJ9
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.6 M sodium/potassium phosphate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0044 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0044 Å / Relative weight: 1
ReflectionResolution: 3.19→46.593 Å / Num. obs: 72155 / % possible obs: 97.5 % / Redundancy: 17.33 % / Rsym value: 0.058 / Net I/σ(I): 62.64
Reflection shellResolution: 3.19→3.39 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 12.7 / % possible all: 91.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VXY

2vxy


Resolution: 3.194→46.593 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2918 3663 5.09 %
Rwork0.2319 --
obs0.2349 71983 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.194→46.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19145 0 80 0 19225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01119309
X-RAY DIFFRACTIONf_angle_d1.42226139
X-RAY DIFFRACTIONf_dihedral_angle_d13.5266649
X-RAY DIFFRACTIONf_chiral_restr0.0763233
X-RAY DIFFRACTIONf_plane_restr0.0073419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.194-3.23610.45871400.37932433X-RAY DIFFRACTION93
3.2361-3.28040.39851390.35062453X-RAY DIFFRACTION93
3.2804-3.32720.3581250.32422481X-RAY DIFFRACTION94
3.3272-3.37690.37571430.30152419X-RAY DIFFRACTION93
3.3769-3.42960.37641090.28892530X-RAY DIFFRACTION95
3.4296-3.48580.34761510.26742558X-RAY DIFFRACTION96
3.4858-3.54590.34221260.26142525X-RAY DIFFRACTION97
3.5459-3.61040.32891360.25562580X-RAY DIFFRACTION98
3.6104-3.67980.27211310.24352605X-RAY DIFFRACTION98
3.6798-3.75490.36321300.23562598X-RAY DIFFRACTION98
3.7549-3.83650.28151500.22432585X-RAY DIFFRACTION98
3.8365-3.92570.28161590.2212597X-RAY DIFFRACTION98
3.9257-4.02380.29991260.22192654X-RAY DIFFRACTION99
4.0238-4.13250.26391360.2242629X-RAY DIFFRACTION99
4.1325-4.25410.29731420.20132665X-RAY DIFFRACTION100
4.2541-4.39130.23921470.1852663X-RAY DIFFRACTION100
4.3913-4.54810.25041370.19142654X-RAY DIFFRACTION100
4.5481-4.730.23141480.18182663X-RAY DIFFRACTION100
4.73-4.94510.28171580.19842683X-RAY DIFFRACTION100
4.9451-5.20540.27271470.21592689X-RAY DIFFRACTION100
5.2054-5.53110.32071410.23512686X-RAY DIFFRACTION100
5.5311-5.95740.28531350.2362729X-RAY DIFFRACTION100
5.9574-6.55540.30531400.24792733X-RAY DIFFRACTION100
6.5554-7.50060.25971460.22722763X-RAY DIFFRACTION100
7.5006-9.43710.24241480.18152808X-RAY DIFFRACTION99
9.4371-46.59810.30261730.27092937X-RAY DIFFRACTION98

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