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- PDB-4asn: TubR from Bacillus megaterium pBM400 -

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Basic information

Entry
Database: PDB / ID: 4asn
TitleTubR from Bacillus megaterium pBM400
ComponentsTUBR
KeywordsTRANSCRIPTION / TUBULIN / FTSZ / SEGREGATION / PARTITION
Function / homologyplasmid partitioning / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / Orthogonal Bundle / Mainly Alpha / DNA-binding protein TubR
Function and homology information
Biological speciesBACILLUS MEGATERIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsAylett, C.H.S. / Lowe, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Superstructure of the Centromeric Complex of Tubzrc Plasmid Partitioning Systems.
Authors: Aylett, C.H.S. / Lowe, J.
History
DepositionMay 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUBR
B: TUBR
C: TUBR


Theoretical massNumber of molelcules
Total (without water)35,1023
Polymers35,1023
Non-polymers00
Water00
1
A: TUBR
B: TUBR


Theoretical massNumber of molelcules
Total (without water)23,4022
Polymers23,4022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-8.1 kcal/mol
Surface area10190 Å2
MethodPISA
2
C: TUBR

C: TUBR


Theoretical massNumber of molelcules
Total (without water)23,4022
Polymers23,4022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area1180 Å2
ΔGint-8.1 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.845, 179.845, 114.342
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 2:91)
211CHAIN B AND (RESSEQ 2:91)
311CHAIN C AND (RESSEQ 2:91)

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Components

#1: Protein TUBR


Mass: 11700.768 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS MEGATERIUM (bacteria) / Strain: QMB 1551 / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q848W2
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: 5.11 Å3/Da / Density % sol: 75.94 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5
Details: BM TUBR CRYSTALS WERE PRODUCED IN 500 NL TO 500 NL PROTEIN TO PRECIPITANT SITTING DROPS: 20 MG/ML BM TUBR, 100 MM TRIS-CL PH 8.5, 0.2 M SODIUM CITRATE, 15 % (V/V) PEG 400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2011
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→46.09 Å / Num. obs: 17357 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Biso Wilson estimate: 125.07 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.1
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameClassification
XDSdata reduction
SCALAdata scaling
SHELXCDEphasing
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.5→46.085 Å / SU ML: 0.29 / σ(F): 1.27 / Phase error: 27.2 / Stereochemistry target values: ML / Details: SHARPENED -50 FOR SIDE CHAIN DENSITY.
RfactorNum. reflection% reflection
Rfree0.2284 902 5.2 %
Rwork0.1858 --
obs0.1879 17357 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 144.55 Å2
Refinement stepCycle: LAST / Resolution: 3.5→46.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 0 0 2184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132226
X-RAY DIFFRACTIONf_angle_d1.3242997
X-RAY DIFFRACTIONf_dihedral_angle_d15.386804
X-RAY DIFFRACTIONf_chiral_restr0.078333
X-RAY DIFFRACTIONf_plane_restr0.004378
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A728X-RAY DIFFRACTIONPOSITIONAL
12B728X-RAY DIFFRACTIONPOSITIONAL0.064
13C728X-RAY DIFFRACTIONPOSITIONAL0.046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.71920.31841650.25962740X-RAY DIFFRACTION100
3.7192-4.00620.24331500.20712739X-RAY DIFFRACTION100
4.0062-4.40910.18941620.15172766X-RAY DIFFRACTION100
4.4091-5.04640.18811460.15712736X-RAY DIFFRACTION100
5.0464-6.35530.23551540.20912739X-RAY DIFFRACTION100
6.3553-46.08930.23861250.18272735X-RAY DIFFRACTION98

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