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- PDB-2vh1: Crystal structure of bacterial cell division protein FtsQ from E.coli -

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Basic information

Entry
Database: PDB / ID: 2vh1
TitleCrystal structure of bacterial cell division protein FtsQ from E.coli
ComponentsCELL DIVISION PROTEIN FTSQ
KeywordsCELL CYCLE / FTSQ / POTRA / MEMBRANE / SEPTATION / CELL DIVISION / TRANSMEMBRANE / INNER MEMBRANE
Function / homology
Function and homology information


FtsQBL complex / divisome complex / division septum assembly / FtsZ-dependent cytokinesis / cell division site / cell division / identical protein binding / plasma membrane
Similarity search - Function
Cell division protein FtsQ/DivIB / Cell division protein FtsQ / Cell division protein FtsQ, C-terminal / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / membrane protein fhac / POTRA domain / POTRA domain profile. ...Cell division protein FtsQ/DivIB / Cell division protein FtsQ / Cell division protein FtsQ, C-terminal / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / membrane protein fhac / POTRA domain / POTRA domain profile. / Ubiquitin-like (UB roll) / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein FtsQ
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
Authorsvan den Ent, F. / Vinkenvleugel, T. / Ind, A. / West, P. / Veprintsev, D. / Naninga, N. / den Blaauwen, T. / Lowe, J.
CitationJournal: Mol.Microbiol. / Year: 2008
Title: Structural and Mutational Analysis of Cell Division Protein Ftsq
Authors: van den Ent, F. / Vinkenvleugel, T. / Ind, A. / West, P. / Veprintsev, D. / Naninga, N. / den Blaauwen, T. / Lowe, J.
History
DepositionNov 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Source and taxonomy / Category: citation_author / entity_src_gen
Item: _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL DIVISION PROTEIN FTSQ
B: CELL DIVISION PROTEIN FTSQ


Theoretical massNumber of molelcules
Total (without water)50,5932
Polymers50,5932
Non-polymers00
Water00
1
A: CELL DIVISION PROTEIN FTSQ


Theoretical massNumber of molelcules
Total (without water)25,2971
Polymers25,2971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELL DIVISION PROTEIN FTSQ


Theoretical massNumber of molelcules
Total (without water)25,2971
Polymers25,2971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)147.844, 147.844, 69.259
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTYRTYRAA58 - 1262 - 70
21SERSERTYRTYRBB58 - 1262 - 70
12PROPROALAALAAA128 - 25772 - 201
22PROPROALAALABB128 - 25772 - 201

NCS oper: (Code: given / Matrix: (1), (0.6), (0.689, -0.725) / Vector: 10)

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Components

#1: Protein CELL DIVISION PROTEIN FTSQ / FTSQ


Mass: 25296.633 Da / Num. of mol.: 2 / Fragment: RESIDUES 58-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P06136

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growDetails: 33 MM N-OCTYL-B-D-GLUCOSIDE, 50 MM TRIS PH8.5, 8% PEG550MME, 8% PEG20K, 1.2 M NAFORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9392
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9392 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 21005 / % possible obs: 98.3 % / Observed criterion σ(I): 2.3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.3 / % possible all: 98.3

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Processing

Software
NameVersionClassification
SHELXDphasing
SHARPphasing
REFMAC5.3.0037refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.7→36.35 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.892 / SU B: 24.332 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1456 6.2 %RANDOM
Rwork0.237 ---
obs0.24 21937 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.29 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å2-0.5 Å20 Å2
2---1 Å20 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.7→36.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 0 0 3234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9584466
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8955396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04923.902164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.61215593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4441531
X-RAY DIFFRACTIONr_chiral_restr0.1070.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022507
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.21246
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.22147
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6563.52041
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01243221
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.06851428
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.666.51245
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1571 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.990.5
medium thermal0.622
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.454 153
Rwork0.41 1610
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
112.0511-2.4761-2.32993.0505-0.81871.11270.12950.62520.2385-0.0901-0.1533-0.2891-0.47610.03190.0239-0.1680.06560.0004-0.0293-0.0466-0.542677.611543.18552.3636
219.81852.1437-2.45792.2327-1.32750.8681-0.00660.7956-0.3266-0.0590.30360.5747-0.31910.0841-0.297-0.03670.22490.0405-0.10290.0229-0.336651.983142.245755.0756
316.4098-3.85114.479114.2016-7.01499.5045-0.07251.0688-0.4817-0.2265-0.27411.46-0.674-0.48490.3467-0.26380.2360.1489-0.0740.1124-0.0340.014942.765257.5379
48.9845-2.83231.68868.7571-2.58986.39140.16420.515-0.9409-0.3225-0.16690.97020.3556-0.00240.0027-0.21160.17510.059-0.03940.05720.296828.041444.13853.7109
510.4566-3.65590.638713.1788-2.98881.385-0.6101-0.9546-1.09371.0217-0.01381.12060.14820.28430.6239-0.05350.00910.19120.2563-0.0480.1135-26.517862.936383.4464
615.1172-8.0336-5.84428.19172.53332.8245-0.0919-0.74710.13920.70290.03590.34150.31950.22840.0559-0.2559-0.05420.0990.0148-0.0756-0.1318-25.12969.047679.5083
711.2256-2.8522-4.21784.8092.46127.9484-0.2953-0.5103-0.94830.47420.08970.14350.6113-0.96180.2057-0.30240.06530.0303-0.10510.0608-0.0897-5.577256.739368.5644
813.0667-4.2816-2.53624.8103-4.688711.9845-0.20540.1238-1.96880.15660.2299-0.62981.32320.3452-0.0245-0.35550.17610.1101-0.1893-0.00550.15295.598453.097763.8722
912.1806-2.6192-0.38971.97353.5158.36090.08980.8153-1.65210.6492-0.0861-0.57211.51190.7417-0.00370.05230.20020.12710.112-0.12370.413411.644547.022155.0391
105.87911.1131-2.78517.4989-8.570611.17540.3161-0.4712-0.93881.3176-0.77170.56870.33290.77850.4556-0.26530.1740.1259-0.09960.10760.411716.996746.403360.9666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A58 - 131
2X-RAY DIFFRACTION2A134 - 183
3X-RAY DIFFRACTION3A185 - 203
4X-RAY DIFFRACTION4A207 - 260
5X-RAY DIFFRACTION5B58 - 82
6X-RAY DIFFRACTION6B85 - 131
7X-RAY DIFFRACTION7B134 - 183
8X-RAY DIFFRACTION8B185 - 203
9X-RAY DIFFRACTION9B207 - 237
10X-RAY DIFFRACTION10B241 - 259

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