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- PDB-4a8c: Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in comp... -

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Entry
Database: PDB / ID: 4a8c
TitleSymmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with a binding peptide
DescriptorPERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
KeywordsHYDROLASE / CHAPERONE
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (7.5 A resolution / Single particle / Vitreous ice)
AuthorsMalet, H. / Canellas, F. / Sawa, J. / Yan, J. / Thalassinos, K. / Ehrmann, M. / Clausen, T. / Saibil, H.R.
CitationNat. Struct. Mol. Biol., 2012, 19, 152-157

Nat. Struct. Mol. Biol., 2012, 19, 152-157 StrPapers
Newly folded substrates inside the molecular cage of the HtrA chaperone DegQ.
Hélène Malet / Flavia Canellas / Justyna Sawa / Jun Yan / Konstantinos Thalassinos / Michael Ehrmann / Tim Clausen / Helen R Saibil

DateDeposition: Nov 20, 2011 / Release: Jan 11, 2012 / Last modification: Feb 15, 2012

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Assembly

Deposited unit
A: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
B: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
C: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
D: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
E: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
F: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
G: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
H: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
I: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
J: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
K: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ
L: PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ


Theoretical massNumber of molelcules
Total (without water)546,51812
Polyers546,51812
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)
PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ / PROTEASE DO / DEGQ


Mass: 45543.152 Da / Num. of mol.: 12 / Mutation: YES
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: P39099, EC: 3.4.21.107

Cellular component

Molecular function

Biological process

Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN C, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN D, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN E, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN F, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN G, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN H, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN I, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN J, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN K, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN L, SER 214 TO ALA

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE

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Sample preparation

Assembly of specimenName: ESCHERICHIA COLI DEGQ 12- MER IN COMPLEX WITH A BINDING PEPTIDE
Aggregation state: PARTICLE
Buffer solutionName: 20 MM HEPES/NAOH, 150 MM NACL
Sample preparationpH: 7.5 / Sample conc.: 0.2 mg/ml
Specimen supportDetails: CARBON
VitrificationDetails: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- MANUAL PLUNGER, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI F20 / Details: LOW DOSE MODE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Specimen holderTemperature: 91 K / Tilt angle max: 0 deg. / Tilt angle min: -0.1 deg.
CameraType: KODAK SO163 FILM
EM image scansNumber digital images: 110
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: IMAGIC-5, SPIDER / Number of particles: 29432
EM single particle entitySymmetry type: MIXED SYMMETRY
3D reconstructionMethod: COMMON LINE, PROJECTION MATCHING / Resolution: 7.5 A / Nominal pixel size: 1.4 A/pix / Actual pixel size: 1.4 A/pix / CTF correction method: PHASE FLIPPING, FULL CTF CORRECTION
Details: DEGQ 12-MER WERE OBTAINED IN PRESENCE OF A PEPTIDE. THE PEPTIDE SEQUENCE IS SPMFKGVLDMMYGGMRGYQV THE NUMBER OF PEPTIDES BOUND TO DEGQ 12-MER IS UNKNOWN. THE PEPTIDES ARE NOT MODELLED DUE TO THE RESOLUTION OF THE MAP. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1983. (DEPOSITION ID: 10374).
Atomic model buildingMethod: RIGID BODY AND FLEXIBLE FITTING / Ref protocol: X-RAY / Ref space: REAL / Target criteria: CROSS-CORRELATION, ENERGY
Atomic model buildingPDB-ID: 3STJ
Least-squares processHighest resolution: 7.5 A
Refine hist #LASTHighest resolution: 7.5 A
Number of atoms included #LASTProtein: 4740 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 4740

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