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- PDB-1jcg: MREB FROM THERMOTOGA MARITIMA, AMPPNP -

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Basic information

Entry
Database: PDB / ID: 1jcg
TitleMREB FROM THERMOTOGA MARITIMA, AMPPNP
ComponentsROD SHAPE-DETERMINING PROTEIN MREB
KeywordsSTRUCTURAL PROTEIN / MreB / rod-shape determining / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 3.1 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 1.3Aug 4, 2021Group: Database references / Derived calculations / Refinement description
Category: refine / struct_ref_seq_dif / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details ..._refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3303
Polymers36,8001
Non-polymers5312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.100, 51.100, 292.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsSame as for 1CJF. One dimensional filaments generated by crystal symmetry; F-actin-like.

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Components

#1: Protein ROD SHAPE-DETERMINING PROTEIN MREB


Mass: 36799.582 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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: 3 Å3/Da / Density % sol: 58.98 %
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 10.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG80001reservoir
2200 mM1reservoirNaCl
30.1 MCAPS1reservoir
48 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 20, 2001 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 8816 / Num. obs: 8166 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 56.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.8
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.219 / % possible all: 99.4

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1CJF

1cjf


Resolution: 3.1→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS 1.0, protein_rep.param
RfactorNum. reflection% reflectionSelection details
Rfree0.2764 377 4.6167 %CNS 1.0, twinning-compatible selection
Rwork0.2056 ---
all0.2056 8816 --
obs0.2056 8166 92.6 %-
Displacement parametersBiso mean: 25.251 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 32 0 2535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.421
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 50 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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