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- PDB-2wus: Bacterial actin MreB assembles in complex with cell shape protein RodZ -

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Basic information

Entry
Database: PDB / ID: 2wus
TitleBacterial actin MreB assembles in complex with cell shape protein RodZ
Components
  • PUTATIVE UNCHARACTERIZED PROTEIN
  • ROD SHAPE-DETERMINING PROTEIN MREB
KeywordsSTRUCTURAL PROTEIN / CELL WALL MORPHOGENESIS / BACTERIAL CYTOSKELETON / BACTERIAL ACTIN / HELIX-TURN-HELIX MOTIF
Function / homology
Function and homology information


cell morphogenesis / regulation of cell shape / membrane => GO:0016020 / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Helix-turn-helix domain / Cell shape determining protein MreB / MreB/Mbl protein / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / Lambda repressor-like, DNA-binding domain superfamily / ATPase, nucleotide binding domain ...Helix-turn-helix domain / Cell shape determining protein MreB / MreB/Mbl protein / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / Lambda repressor-like, DNA-binding domain superfamily / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cell shape-determining protein MreB / Uncharacterized protein
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
Authorsvan den Ent, F. / Johnson, C.M. / Persons, L. / deBoer, P. / Lowe, J.
CitationJournal: Embo J. / Year: 2010
Title: Bacterial Actin Mreb Assembles in Complex with Cell Shape Protein Rodz.
Authors: van den Ent, F. / Johnson, C.M. / Persons, L. / deBoer, P. / Lowe, J.
History
DepositionOct 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 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 1.4Dec 20, 2023Group: 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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ROD SHAPE-DETERMINING PROTEIN MREB
B: ROD SHAPE-DETERMINING PROTEIN MREB
R: PUTATIVE UNCHARACTERIZED PROTEIN
S: PUTATIVE UNCHARACTERIZED PROTEIN


Theoretical massNumber of molelcules
Total (without water)100,6244
Polymers100,6244
Non-polymers00
Water0
1
A: ROD SHAPE-DETERMINING PROTEIN MREB
R: PUTATIVE UNCHARACTERIZED PROTEIN


Theoretical massNumber of molelcules
Total (without water)50,3122
Polymers50,3122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ROD SHAPE-DETERMINING PROTEIN MREB
S: PUTATIVE UNCHARACTERIZED PROTEIN


Theoretical massNumber of molelcules
Total (without water)50,3122
Polymers50,3122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.813, 109.836, 112.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein ROD SHAPE-DETERMINING PROTEIN MREB / MREB


Mass: 36799.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9WZ57
#2: Protein PUTATIVE UNCHARACTERIZED PROTEIN / RODZ


Mass: 13512.406 Da / Num. of mol.: 2 / Fragment: HELIX_TURN_HELIX DOMAIN, RESIDUES 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9X2H8

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 12% PEG 1000 MME, 478 MM SODIUM THIOCYANATE, 147 MM CACL2, 100 MM TRIS-HCL, PH 7.7, 6.5% ETOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 19032 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 41.27 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.5
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.7 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JCE

1jce


Resolution: 2.9→39.256 Å / SU ML: 0.46 / σ(F): 1.04 / Phase error: 28.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2878 1983 5.1 %
Rwork0.1972 --
obs0.2017 19032 90.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.449 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.3001 Å2-0 Å20 Å2
2---12.9872 Å20 Å2
3---8.3418 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 0 0 6399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096465
X-RAY DIFFRACTIONf_angle_d1.2338715
X-RAY DIFFRACTIONf_dihedral_angle_d20.1792471
X-RAY DIFFRACTIONf_chiral_restr0.0781049
X-RAY DIFFRACTIONf_plane_restr0.0041111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-2.97260.39651480.29082690X-RAY DIFFRACTION93
2.9726-3.05290.36821480.26112775X-RAY DIFFRACTION93
3.0529-3.14270.36451450.24382690X-RAY DIFFRACTION92
3.1427-3.24410.30691410.22592709X-RAY DIFFRACTION92
3.2441-3.360.30451310.21612688X-RAY DIFFRACTION92
3.36-3.49440.3341330.20792704X-RAY DIFFRACTION91
3.4944-3.65340.35131120.19572759X-RAY DIFFRACTION92
3.6534-3.84580.29911280.18662673X-RAY DIFFRACTION91
3.8458-4.08660.28691610.18042658X-RAY DIFFRACTION91
4.0866-4.40170.27441350.14852661X-RAY DIFFRACTION91
4.4017-4.84390.20511730.1282640X-RAY DIFFRACTION91
4.8439-5.54320.21511530.1342644X-RAY DIFFRACTION91
5.5432-6.97740.21961460.16542562X-RAY DIFFRACTION88
6.9774-39.26010.2351290.16932449X-RAY DIFFRACTION83
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)
10.97460.20630.84490.82930.65521.8408-0.0776-0.10910.04090.1516-0.1910.05040.2301-0.06790.09190.18190.03670.02490.15220.01660.033131.619213.532249.164
20.98851.2448-0.01592.48830.08980.9085-0.1034-0.31070.3412-0.256-0.10550.4370.2876-0.05220.22470.25750.1106-0.06310.139-0.06630.132539.6197-1.042735.7104
30.6559-0.5101-0.25431.16720.71330.347-0.0759-0.0302-0.1507-0.15910.08390.1672-0.12390.0744-0.0370.0471-0.00690.03230.11480.0340.063639.062724.997127.3107
40.994-0.1180.87020.8398-0.17831.4321-0.18360.11540.4297-0.259-0.2426-0.3839-0.6106-0.02020.16980.3662-0.01870.11280.06130.16020.1831-2.738436.35544.9029
50.46190.1629-0.02071.88561.31931.0508-0.09190.0120.10750.3743-0.0803-0.11880.1827-0.0953-0.07980.1286-0.0061-0.05940.10060.05640.0584-1.829425.685628.5051
60.7772-0.24630.48221.3454-0.00430.38150.2081-0.19180.01090.309-0.2113-0.3775-0.00140.0691-0.0167-0.0118-0.029-0.00870.16270.02480.095945.130748.118343.6911
70.6291-0.0130.11421.26180.83721.09660.21110.22160.09850.21570.3119-0.69110.06630.0802-0.3320.0730.0515-0.05670.0954-0.05860.28249.80822.033515.5932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2:32 OR RESID 73:140 OR RESID 312:336 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 33:72 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 141:311 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 4:32 OR RESID 73:140 OR RESID 312:336 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 141:311 )
6X-RAY DIFFRACTION6CHAIN R
7X-RAY DIFFRACTION7CHAIN S

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