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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 / homologySHS2 domain inserted in FtsA / Cell division protein FtsA / SHS2 domain inserted in FTSA / Cell division protein FtsA / FtsZ-dependent cytokinesis / cell division site / cytoplasmic side of plasma membrane / cell division / ATP binding / identical protein binding / Cell division protein FtsA
Function and homology information
Specimen sourceTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 2.6 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 3, 2000 / Release: Oct 18, 2000
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 18, 2000Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jan 24, 2018Structure modelDatabase references / Source and taxonomy / Structure summaryaudit_author / citation_author / entity_src_gen_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

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Assembly

Deposited unit
T: CELL DIVISION PROTEIN FTSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9353
Polyers47,4041
Non-polymers5312
Water1,24369
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
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-MP 1 21 1

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Components

#1: Protein/peptide CELL DIVISION PROTEIN FTSA /


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


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Formula: H2O / Water

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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 / Density percent sol: 42 %
Crystal growpH: 5.5
Details: 200 MM AMMONIUM ACETATE, 100 MM NA ACETATE PH 5.5, 15% PEG
Crystal grow
*PLUS
Temp: 18 ℃ / Method: vapor diffusion, sitting drop
components of the solutions
*PLUS
IDConcCommon 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: 1 kelvins
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE ID14-4 / Synchrotron site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393, 0.9787, 0.9791
DetectorCollection date: Feb 15, 2000
RadiationDiffraction protocol: MAD / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
10.93931.0
20.97871.0
30.97911.0
ReflectionB iso Wilson estimate: 55.8 Å2 / D resolution high: 2.6 Å / D resolution low: 3 Å / Number obs: 11678 / Rmerge I obs: 0.066 / NetI over sigmaI: 18.1 / Redundancy: 6.2 % / Percent possible obs: 97.9
Reflection shellRmerge I obs: 0.235 / Highest resolution: 2.6 Å / Lowest resolution: 2.74 Å / MeanI over sigI obs: 5.9 / Redundancy: 5.8 % / Percent possible all: 98.1
Reflection shell
*PLUS
Percent possible obs: 98.1

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Processing

Software
NameVersionClassification
CNS1.0refinement
CNS1.0phasing
RefineMethod to determine structure: MAD / R Free selection details: RANDOM / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / Sigma F: 0
Solvent computationSolvent model details: FLAT MODEL
Displacement parametersB iso mean: 43.27 Å2 / Aniso B11: 3.52 Å2 / Aniso B12: 0 Å2 / Aniso B13: -1.53 Å2 / Aniso B22: -5.84 Å2 / Aniso B23: 0 Å2 / Aniso B33: 2.315 Å2
Least-squares processR factor R free: 0.282 / R factor R work: 0.22 / R factor obs: 0.22 / Highest resolution: 2.6 Å / Lowest resolution: 3 Å / Number reflection R free: 581 / Number reflection obs: 11678 / Percent reflection R free: 5 / Percent reflection obs: 97.9
Refine hist #LASTHighest resolution: 2.6 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 2988 / Nucleic acid: 0 / Ligand: 32 / Solvent: 69 / Total: 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_it0.01.5
X-RAY DIFFRACTIONc_mcangle_it0.02.0
X-RAY DIFFRACTIONc_scbond_it0.02.0
X-RAY DIFFRACTIONc_scangle_it0.02.5
Refine LS shellHighest resolution: 2.6 Å / R factor R free: 0.467 / R factor R work: 0.323 / Lowest resolution: 2.68 Å / Number reflection R free: 65 / Number reflection R work: 978 / Total number of bins used: 11 / Percent reflection R free: 5

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