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- PDB-1lv7: Crystal Structure of the AAA domain of FtsH -

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Basic information

Entry
Database: PDB / ID: 1lv7
TitleCrystal Structure of the AAA domain of FtsH
ComponentsFtsH
KeywordsHYDROLASE / ALPHA/BETA DOMAIN / FOUR HELIX BUNDLE
Function / homology
Function and homology information


membrane protein complex / plasma membrane protein complex / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / plasma membrane
Similarity search - Function
Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site ...Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP-dependent zinc metalloprotease FtsH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å
AuthorsKrzywda, S. / Brzozowski, A.M. / Verma, C. / Karata, K. / Ogura, T. / Wilkinson, A.J.
Citation
Journal: Structure / Year: 2002
Title: The crystal structure of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli at 1.5 A resolution.
Authors: Krzywda, S. / Brzozowski, A.M. / Verma, C. / Karata, K. / Ogura, T. / Wilkinson, A.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli
Authors: Krzywda, S. / Brzozowski, A.M. / Karata, K. / Ogura, T. / Wilkinson, A.J.
History
DepositionMay 26, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FtsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2496
Polymers27,7691
Non-polymers4805
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: FtsH
hetero molecules

A: FtsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,49912
Polymers55,5382
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6090 Å2
ΔGint-154 kcal/mol
Surface area22760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.152, 53.152, 189.066
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1263-

HOH

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Components

#1: Protein FtsH / Cell division protein ftsH


Mass: 27769.084 Da / Num. of mol.: 1 / Fragment: AAA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FTSH / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P0AAI3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulfate, Tris-HCl, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.5
250 mM1dropNaCl
31 mMdithiothreitol1drop
410 mg/mlprotein1drop
50.1 MTris-HCl1reservoirpH8.5
61.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. obs: 44655 / % possible obs: 98.4 % / Num. measured all: 913258 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.55 Å / % possible obs: 91.1 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5.1.12refinement
RefinementMethod to determine structure: MIRAS / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.129 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17796 2198 5 %RANDOM
Rwork0.15361 ---
obs0.15488 41544 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.559 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--1.01 Å20 Å2
3----2.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 25 366 2291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221977
X-RAY DIFFRACTIONr_bond_other_d0.0020.021878
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.9882656
X-RAY DIFFRACTIONr_angle_other_deg2.09834371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022174
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02385
X-RAY DIFFRACTIONr_nbd_refined0.2230.2393
X-RAY DIFFRACTIONr_nbd_other0.260.22103
X-RAY DIFFRACTIONr_nbtor_other0.0950.21116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.3381.51239
X-RAY DIFFRACTIONr_mcangle_it1.91321993
X-RAY DIFFRACTIONr_scbond_it2.6393738
X-RAY DIFFRACTIONr_scangle_it3.824.5663
X-RAY DIFFRACTIONr_rigid_bond_restr1.48621977
X-RAY DIFFRACTIONr_sphericity_free5.5132366
X-RAY DIFFRACTIONr_sphericity_bonded2.5921955
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 132 -
Rwork0.22 2677 -
obs--91.1 %
Refinement TLS params.Method: refined / Origin x: 19.9861 Å / Origin y: 21.6216 Å / Origin z: 55.3517 Å
111213212223313233
T0.0095 Å20.0118 Å2-0.0174 Å2-0.0192 Å2-0.0067 Å2--0.0799 Å2
L0.4436 °20.1001 °20.078 °2-0.6263 °20.7367 °2--1.9477 °2
S0.0219 Å °-0.0711 Å °-0.0236 Å °0.0805 Å °-0.0325 Å °0.0801 Å °0.2079 Å °-0.141 Å °0.0106 Å °
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. reflection obs: 421544 / % reflection Rfree: 5 % / Rfactor obs: 0.15488 / Rfactor Rfree: 0.178 / Rfactor Rwork: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.811
LS refinement shell
*PLUS
Rfactor Rfree: 0.239 / Rfactor Rwork: 0.22

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