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- PDB-4m8a: Crystal Structure of Thermotoga maritima FtsH Periplasmic Domain -

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Basic information

Entry
Database: PDB / ID: 4m8a
TitleCrystal Structure of Thermotoga maritima FtsH Periplasmic Domain
ComponentsATP-dependent zinc metalloprotease FtsH
KeywordsHYDROLASE / Protease / ATP-dependent proteolysis / Open-closed gating / periplasmic innermembrane
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 M41 / Peptidase, FtsH / 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 M41 / Peptidase, FtsH / 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: 1.502 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: Structural roles of periplasmic and transmembrane domains of FtsH in ATP-dependent proteolysis
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
DepositionAug 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
C: ATP-dependent zinc metalloprotease FtsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1314
Polymers24,0093
Non-polymers1221
Water4,197233
1
A: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
C: ATP-dependent zinc metalloprotease FtsH
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)48,2638
Polymers48,0186
Non-polymers2442
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)41.809, 65.837, 71.834
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
11A-862-

HOH

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Components

#1: Protein ATP-dependent zinc metalloprotease FtsH


Mass: 8003.043 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 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9WZ49, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.0640.26
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2941vapor diffusion5.525% PEG 3350, 0.1M Na citrate (pH 5.5), 0.2M Li2SO4 , VAPOR DIFFUSION, temperature 294K
2942vapor diffusion615%(w/v) PEG 2000, 0.1M MES-NaOH (pH 6.0) , VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97924, 0.97901, 0.97134, 0.98696
DetectorType: ADSC QUANTUM 315r / 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: 1.5→31.7 Å / Num. all: 32191 / Num. obs: 32191 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 27.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 13 / Num. unique all: 1584 / Rsym value: 0.253 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.502→31.677 Å / SU ML: 0.37 / σ(F): 1.91 / Phase error: 17.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 1631 5.07 %random
Rwork0.1609 ---
obs0.1649 32151 99.3 %-
all-32191 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.019 Å2 / ksol: 0.394 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4299 Å20 Å20 Å2
2---1.7387 Å2-0 Å2
3---1.3088 Å2
Refinement stepCycle: LAST / Resolution: 1.502→31.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 0 8 233 1849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071749
X-RAY DIFFRACTIONf_angle_d1.0282377
X-RAY DIFFRACTIONf_dihedral_angle_d13.624678
X-RAY DIFFRACTIONf_chiral_restr0.073272
X-RAY DIFFRACTIONf_plane_restr0.004309
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5017-1.54590.25561290.1796241897
1.5459-1.59580.21051490.15072502100
1.5958-1.65280.21511360.15382527100
1.6528-1.7190.21171430.14362511100
1.719-1.79720.24671250.1312550100
1.7972-1.8920.17171180.12452566100
1.892-2.01050.21621360.1412514100
2.0105-2.16570.17441320.14812578100
2.1657-2.38360.18471420.15342541100
2.3836-2.72830.18721350.16282590100
2.7283-3.43670.23511520.17362590100
3.4367-31.68390.21331340.1867263396

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