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- PDB-1e4g: FtsA (ATP-bound form) from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1e4g
TitleFtsA (ATP-bound form) from Thermotoga maritima
ComponentsCELL DIVISION PROTEIN FTSA
KeywordsBACTERIAL CELL DIVISION / ACTIN FAMILY
Function / homology
Function and homology information


FtsZ-dependent cytokinesis / cell division site / cytoplasmic side of plasma membrane / cell division / ATP binding / identical protein binding
Similarity search - Function
Dna Ligase; domain 1 - #110 / Cell division protein FtsA / SHS2 domain inserted in FTSA / Cell division protein FtsA / SHS2 domain inserted in FtsA / Cell division protein FtsA / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Dna Ligase; domain 1 ...Dna Ligase; domain 1 - #110 / Cell division protein FtsA / SHS2 domain inserted in FTSA / Cell division protein FtsA / SHS2 domain inserted in FtsA / Cell division protein FtsA / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Dna Ligase; domain 1 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Cell division protein FtsA
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
Authorsvan den Ent, F. / Lowe, J.
CitationJournal: Embo J. / Year: 2000
Title: Crystal Structure of the Cell Division Protein Ftsa from Thermotoga Maritima
Authors: van den Ent, F. / Lowe, J.
History
DepositionJul 3, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2000Provider: 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 / Structure summary
Category: audit_author / citation_author / entity_src_gen
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: CELL DIVISION PROTEIN FTSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9353
Polymers47,4041
Non-polymers5312
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.450, 73.740, 57.040
Angle α, β, γ (deg.)90.00, 113.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CELL DIVISION PROTEIN FTSA /


Mass: 47404.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Gene: FTSA / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9WZU0
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.05 Å3/Da / Density % sol: 42 %
Crystal growpH: 5.5
Details: 200 MM AMMONIUM ACETATE, 100 MM NA ACETATE PH 5.5, 15% PEG
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113 mg/mlprotein1drop
21 mMADP1drop
32 mM1dropMgCl2
4200 mMammonium acetate1reservoir
5100 mMsodium acetate1reservoir
615 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393, 0.9787, 0.9791
DetectorDate: Feb 15, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93931
20.97871
30.97911
ReflectionResolution: 2.6→30 Å / Num. obs: 11678 / % possible obs: 97.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 18.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 5.9 / % possible all: 98.1
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameVersionClassification
CNS1refinement
CNS1phasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→30 Å / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 581 5 %RANDOM
Rwork0.22 ---
obs0.22 11678 97.9 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 43.27 Å2
Baniso -1Baniso -2Baniso -3
1-3.52 Å20 Å2-1.53 Å2
2---5.84 Å20 Å2
3---2.315 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 32 69 3089
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.376
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it02
X-RAY DIFFRACTIONc_scangle_it02.5
LS refinement shellResolution: 2.6→2.68 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.467 65 5 %
Rwork0.323 978 -

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