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- PDB-4czi: C. crescentus MreB, single filament, empty -

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Basic information

Entry
Database: PDB / ID: 4czi
TitleC. crescentus MreB, single filament, empty
ComponentsROD SHAPE-DETERMINING PROTEIN MREB
KeywordsSTRUCTURAL PROTEIN / BACTERIAL ACTIN / BACTERIAL CYTOSKELETON
Function / homology
Function and homology information


cell morphogenesis / regulation of cell shape / ATP binding / cytoplasm
Similarity search - Function
Cell shape determining protein MreB / : / MreB/Mbl protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell shape-determining protein MreB / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesCAULOBACTER VIBRIOIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLowe, J. / vandenEnt, F.
CitationJournal: Elife / Year: 2014
Title: Bacterial Actin Mreb Forms Antiparallel Double Filaments.
Authors: Van Den Ent, F. / Izore, T. / Bharat, T.A. / Johnson, C.M. / Lowe, J.
History
DepositionApr 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Atomic model / Database references / Other
Revision 1.2Dec 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


Theoretical massNumber of molelcules
Total (without water)36,8651
Polymers36,8651
Non-polymers00
Water5,549308
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.951, 69.238, 52.183
Angle α, β, γ (deg.)90.00, 99.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36865.496 Da / Num. of mol.: 1 / Fragment: RESIDUES 9-347 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: M-I9-CCMREB(F102S, V103G)-A347-GSHHHHHH / Source: (gene. exp.) CAULOBACTER VIBRIOIDES (bacteria) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: B8H609, UniProt: A0A0H3C7V4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 33485 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 120.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.2 / % possible all: 99.1

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Processing

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

1jce


Resolution: 1.8→41.182 Å / SU ML: 0.43 / σ(F): 1.2 / Phase error: 21.53 / Stereochemistry target values: ML3
RfactorNum. reflection% reflection
Rfree0.2169 3159 5 %
Rwork0.1842 --
obs0.1858 33573 95.1 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.096 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.6867 Å2-0 Å2-2.2187 Å2
2--2.9341 Å20 Å2
3---3.7527 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 0 308 2643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112360
X-RAY DIFFRACTIONf_angle_d1.2983186
X-RAY DIFFRACTIONf_dihedral_angle_d13.322894
X-RAY DIFFRACTIONf_chiral_restr0.075381
X-RAY DIFFRACTIONf_plane_restr0.006416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82690.27821280.26082492X-RAY DIFFRACTION92
1.8269-1.85550.25031530.24772556X-RAY DIFFRACTION92
1.8555-1.88590.25351520.23472503X-RAY DIFFRACTION93
1.8859-1.91840.21891440.20912625X-RAY DIFFRACTION93
1.9184-1.95330.2521990.19942509X-RAY DIFFRACTION93
1.9533-1.99080.23851780.19422542X-RAY DIFFRACTION94
1.9908-2.03150.24291450.19952560X-RAY DIFFRACTION94
2.0315-2.07570.25311270.1932589X-RAY DIFFRACTION94
2.0757-2.12390.23621500.19342544X-RAY DIFFRACTION95
2.1239-2.1770.24441540.18582642X-RAY DIFFRACTION94
2.177-2.23590.23611240.18742584X-RAY DIFFRACTION95
2.2359-2.30170.2321230.18192623X-RAY DIFFRACTION95
2.3017-2.3760.23651190.18672641X-RAY DIFFRACTION95
2.376-2.46090.21671440.16992609X-RAY DIFFRACTION95
2.4609-2.55940.25771210.17342618X-RAY DIFFRACTION96
2.5594-2.67590.19321230.17342690X-RAY DIFFRACTION96
2.6759-2.81690.24081400.18312631X-RAY DIFFRACTION97
2.8169-2.99340.20281650.18782668X-RAY DIFFRACTION97
2.9934-3.22440.2061440.18372664X-RAY DIFFRACTION97
3.2244-3.54870.21731420.18242661X-RAY DIFFRACTION98
3.5487-4.06180.1731420.17312688X-RAY DIFFRACTION97
4.0618-5.1160.17481140.15442706X-RAY DIFFRACTION98
5.116-41.19290.22721280.19552678X-RAY DIFFRACTION97

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