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

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Basic information

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 Å resolution / Particle / Single particle)
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 20, 2011 / Release: Jan 11, 2012
RevisionDateData content typeGroupProviderType
1.0Jan 11, 2012Structure modelrepositoryInitial release
1.1Feb 15, 2012Structure modelOther

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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)546,51212
Polyers546,51212
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 / Coordinate model: Cα atoms only


Mass: 45542.664 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 experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: ESCHERICHIA COLI DEGQ 12- MER IN COMPLEX WITH A BINDING PEPTIDE
Type: COMPLEX
Buffer solutionName: 20 MM HEPES/NAOH, 150 MM NACL / Details: 20 MM HEPES/NAOH, 150 MM NACL / pH: 7.5
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- MANUAL PLUNGER, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20 / Details: LOW DOSE MODE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Calibrated magnification: 50000 / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Specimen holderTemperature: 91 kelvins / Tilt angle max: 0 deg. / Tilt angle min: -0.1 deg.
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 110
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1FlexEMMODEL FITTING
2ModellerMODEL FITTING
3UCSF ChimeraMODEL FITTING
4IMAGIC5RECONSTRUCTION
5SPIDERRECONSTRUCTION
CTF correctionDetails: PHASE FLIPPING, FULL CTF CORRECTION
SymmetryPoint symmetry: D3
3D reconstructionMethod: COMMON LINE, PROJECTION MATCHING / Resolution: 7.5 Å / Number of particles: 29432 / Nominal pixel size: 1.4 / Actual pixel size: 1.4
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).
Symmetry type: POINT
Atomic model buildingDetails: METHOD--RIGID BODY AND FLEXIBLE FITTING REFINEMENT PROTOCOL--X-RAY
Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: CROSS-CORRELATION, ENERGY
Atomic model buildingPDB-ID: 3STJ
Least-squares processHighest resolution: 7.5 Å
Refine hist #LASTHighest resolution: 7.5 Å
Number of atoms included #LASTProtein: 4740 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 4740

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