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- PDB-1jce: MREB FROM THERMOTOGA MARITIMA -

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Basic information

Entry
Database: PDB / ID: 1jce
TitleMREB FROM THERMOTOGA MARITIMA
ComponentsROD SHAPE-DETERMINING PROTEIN MREB
KeywordsSTRUCTURAL PROTEIN / rod-shape determining / MreB / Mbl / actin / hsp-70 / ftsz
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
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
Authorsvan den Ent, F. / Amos, L.A. / Lowe, J.
CitationJournal: Nature / Year: 2001
Title: Prokaryotic origin of the actin cytoskeleton.
Authors: van den Ent, F. / Amos, L.A. / Lowe, J.
History
DepositionJun 9, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ROD SHAPE-DETERMINING PROTEIN MREB


Theoretical massNumber of molelcules
Total (without water)37,1751
Polymers37,1751
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.63, 70.13, 82.18
Angle α, β, γ (deg.)90, 108.79, 90
Int Tables number5
Space group name H-MC121
DetailsCrystal symmetry generates one-dimensional filaments. These filaments are similar to one of the strands of F-actin (protofilament)

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Components

#1: Protein ROD SHAPE-DETERMINING PROTEIN MREB


Mass: 37174.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0588 / Plasmid: PHIS17 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q9WZ57
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
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: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %isopropanol1reservoir
2200 mM1reservoirNaCl
30.1 MHEPES1reservoir
48 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9780, 0.9802, 0.9394
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 8, 2001
RadiationMonochromator: double / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.98021
30.93941
ReflectionResolution: 2.1→50 Å / Num. all: 24183 / Num. obs: 22453 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.239 / % possible all: 67.5

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Processing

Software
NameVersionClassification
SOLVEphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS 1.0, protein_rep.param
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 1127 5.019 %random
Rwork0.1973 ---
all0.1973 24183 --
obs0.1973 22453 --
Displacement parametersBiso mean: 28.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 0 266 2747
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.233
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 50 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.6 Å2

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