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- PDB-4q0f: Crystal Structure of Thermotoga maritima FtsH Periplasmic domain -

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Basic information

Entry
Database: PDB / ID: 4q0f
TitleCrystal Structure of Thermotoga maritima FtsH Periplasmic domain
ComponentsATP-dependent zinc metalloprotease FtsH
KeywordsHYDROLASE / ATP-dependent proteolysis
Function / homology
Function and homology information


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 / identical protein binding / plasma membrane
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #210 / Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase, FtsH / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / AAA ATPase, AAA+ lid domain / AAA+ lid domain ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #210 / Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase, FtsH / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent zinc metalloprotease FtsH
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.948 Å
AuthorsAn, J.Y. / Sharif, H. / Barrera, F.N. / Karabadzhak, A. / Kang, G.B. / Park, K.J. / Sakkiah, S. / Lee, K.W. / Lee, S. / Engelman, D.M. ...An, J.Y. / Sharif, H. / Barrera, F.N. / Karabadzhak, A. / Kang, G.B. / Park, K.J. / Sakkiah, S. / Lee, K.W. / Lee, S. / Engelman, D.M. / Wang, J. / Eom, S.H.
CitationJournal: To be Published
Title: Structures of periplasmic and transmembrane domains of FtsH suggest a reverse translocon mechanism for protein extraction from membrane
Authors: An, J.Y. / Sharif, H. / Barrera, F.N. / Karabadzhak, A. / Kang, G.B. / Park, K.J. / Sakkiah, S. / Lee, K.W. / Lee, S. / Engelman, D.M. / Wang, J. / Eom, S.H.
History
DepositionApr 1, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
C: ATP-dependent zinc metalloprotease FtsH


Theoretical massNumber of molelcules
Total (without water)24,2913
Polymers24,2913
Non-polymers00
Water1,56787
1
A: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
C: ATP-dependent zinc metalloprotease FtsH

A: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
C: ATP-dependent zinc metalloprotease FtsH


Theoretical massNumber of molelcules
Total (without water)48,5816
Polymers48,5816
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Unit cell
Length a, b, c (Å)42.032, 66.125, 72.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-239-

HOH

21B-241-

HOH

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Components

#1: Protein ATP-dependent zinc metalloprotease FtsH


Mass: 8096.834 Da / Num. of mol.: 3 / Fragment: periplasmic domain, UNP RESIDUES 34-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: ftsH, TM_0580 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZ49, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% (w/v) PEG 2000, 0.1M MES-NaOH (pH 6.0) , VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97924, 0.97901, 0.97134, 0.98696
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.979011
30.971341
40.986961
ReflectionResolution: 1.948→50 Å / Num. all: 15227 / Num. obs: 15191 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→1.98 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.948→36.304 Å / SU ML: 0.21 / σ(F): 1.01 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 756 5.01 %RANDOM
Rwork0.2091 ---
all0.2112 15227 --
obs0.2112 15081 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.948→36.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 0 87 1686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031617
X-RAY DIFFRACTIONf_angle_d0.6392182
X-RAY DIFFRACTIONf_dihedral_angle_d12.621609
X-RAY DIFFRACTIONf_chiral_restr0.045256
X-RAY DIFFRACTIONf_plane_restr0.002276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9475-2.09790.28461340.2334273797
2.0979-2.30890.28871870.2394278499
2.3089-2.6430.25211480.21582878100
2.643-3.32950.24531610.21382885100
3.3295-36.30980.23621260.1902304199

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