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- PDB-3stj: Crystal structure of the protease + PDZ1 domain of DegQ from Esch... -

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Basic information

Entry
Database: PDB / ID: 3stj
TitleCrystal structure of the protease + PDZ1 domain of DegQ from Escherichia coli
Components
  • Protease degQ
  • peptide (UNK)
KeywordsHYDROLASE / serine protease / PDZ domain / protease / chaperone / DegP / DegQ
Function / homology
Function and homology information


peptidase Do / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidase activity / periplasmic space / serine-type endopeptidase activity / identical protein binding
Similarity search - Function
Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Periplasmic pH-dependent serine endoprotease DegQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSawa, J. / Malet, H. / Krojer, T. / Canellas, F. / Ehrmann, M. / Clausen, T.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular adaptation of the DegQ protease to exert protein quality control in the bacterial cell envelope.
Authors: Sawa, J. / Malet, H. / Krojer, T. / Canellas, F. / Ehrmann, M. / Clausen, T.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease degQ
B: Protease degQ
C: Protease degQ
D: Protease degQ
E: Protease degQ
F: Protease degQ
G: Protease degQ
H: Protease degQ
I: Protease degQ
J: Protease degQ
K: Protease degQ
L: Protease degQ
M: peptide (UNK)
N: peptide (UNK)
O: peptide (UNK)
P: peptide (UNK)
Q: peptide (UNK)
R: peptide (UNK)
S: peptide (UNK)
T: peptide (UNK)
U: peptide (UNK)
V: peptide (UNK)
W: peptide (UNK)
X: peptide (UNK)
Z: peptide (UNK)


Theoretical massNumber of molelcules
Total (without water)440,07025
Polymers440,07025
Non-polymers00
Water0
1
A: Protease degQ
B: Protease degQ
C: Protease degQ
M: peptide (UNK)
N: peptide (UNK)
O: peptide (UNK)
Z: peptide (UNK)


Theoretical massNumber of molelcules
Total (without water)110,4787
Polymers110,4787
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-47 kcal/mol
Surface area35820 Å2
MethodPISA
2
D: Protease degQ
E: Protease degQ
F: Protease degQ
P: peptide (UNK)
Q: peptide (UNK)
R: peptide (UNK)


Theoretical massNumber of molelcules
Total (without water)109,8646
Polymers109,8646
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-38 kcal/mol
Surface area35960 Å2
MethodPISA
3
G: Protease degQ
H: Protease degQ
I: Protease degQ
S: peptide (UNK)
T: peptide (UNK)
U: peptide (UNK)


Theoretical massNumber of molelcules
Total (without water)109,8646
Polymers109,8646
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-38 kcal/mol
Surface area35860 Å2
MethodPISA
4
J: Protease degQ
K: Protease degQ
L: Protease degQ
V: peptide (UNK)
W: peptide (UNK)
X: peptide (UNK)


Theoretical massNumber of molelcules
Total (without water)109,8646
Polymers109,8646
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-38 kcal/mol
Surface area35940 Å2
MethodPISA
5
D: Protease degQ
E: Protease degQ
F: Protease degQ
P: peptide (UNK)
Q: peptide (UNK)
R: peptide (UNK)

J: Protease degQ
K: Protease degQ
L: Protease degQ
V: peptide (UNK)
W: peptide (UNK)
X: peptide (UNK)

G: Protease degQ
H: Protease degQ
I: Protease degQ
S: peptide (UNK)
T: peptide (UNK)
U: peptide (UNK)

A: Protease degQ
B: Protease degQ
C: Protease degQ
M: peptide (UNK)
N: peptide (UNK)
O: peptide (UNK)
Z: peptide (UNK)


Theoretical massNumber of molelcules
Total (without water)440,07025
Polymers440,07025
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_565-y,x-y+1,z+1/31
identity operation1_555x,y,z1
Buried area46990 Å2
ΔGint-181 kcal/mol
Surface area130500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.316, 115.316, 287.419
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsAS PER THE AUTHORS THE PROTEIN IS ONLY PRESENT AS A TRIMER IN SOLUTION IN THE ABSENCE OF SUBSTRATES

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Components

#1: Protein
Protease degQ


Mass: 36007.609 Da / Num. of mol.: 12 / Fragment: UNP residues 28-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: degQ, hhoA, b3234, JW3203 / Production host: Escherichia coli (E. coli)
References: UniProt: P39099, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide
peptide (UNK)


Mass: 613.749 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
Compound detailsTHE PRESENCE OF THE UNKNOWN PEPTIDE CANNOT BE DISPUTED. THESE CHAINS HAVE WEAK ELECTRON DENSITY AND ...THE PRESENCE OF THE UNKNOWN PEPTIDE CANNOT BE DISPUTED. THESE CHAINS HAVE WEAK ELECTRON DENSITY AND HIGH B-FACTORS. THEIR PRESENCE BECAME EVIDENT FROM INSPECTION OF DIFFERENCE ELECTRON DENSITY MAPS AND FITS WELL TO SIMILAR OBSERVATIONS IN HOMOLOGOUS STRUCTURES. THEIR POOR DEFINITION MAY REFLECT THE FACT THAT THESE PEPTIDE WERE NOT ADDED AT ANY STEP OF THE PROTEIN PREPARATION OR CRYSTALLIZATION TRIALS, HENCE THEY MUST HAVE BEEN PICKED UP FROM THE EXPRESSION SYSTEM OR BE A CONSEQUENCE OF SOME FORM OF PROTEOLYSIS. THEREFORE THEIR OCCUPANCY IS PROBABLY LOW

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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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.4
Details: 24% PEG6000, 5% PEG100, 10% glycerol, 0.1M MES pH5.4, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 124692 / Num. obs: 124692 / % possible obs: 95.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 68.23 Å2

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.8.0refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.94 Å / Cor.coef. Fo:Fc: 0.9428 / Cor.coef. Fo:Fc free: 0.9292 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 6289 5.04 %RANDOM
Rwork0.1843 ---
all0.1857 124692 --
obs0.1857 124692 --
Displacement parametersBiso mean: 60.28 Å2
Baniso -1Baniso -2Baniso -3
1-3.4936 Å20 Å20 Å2
2--3.4936 Å20 Å2
3----6.9873 Å2
Refine analyzeLuzzati coordinate error obs: 0.348 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26483 0 0 0 26483
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0126770HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3236202HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12553SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes744HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3906HARMONIC5
X-RAY DIFFRACTIONt_it26770HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion3.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3691SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact28646SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2481 384 4.73 %
Rwork0.2213 7727 -
all0.2225 8111 -

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