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- PDB-7xw0: Crystal structure of pOmpT -

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Basic information

Entry
Database: PDB / ID: 7xw0
TitleCrystal structure of pOmpT
ComponentsOmpT
KeywordsHYDROLASE / out membrane protein / protease
Function / homology
Function and homology information


omptin / cell outer membrane / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase A26, omptin / Peptidase A26, omptin, conserved site / : / Omptin family / Aspartyl proteases, omptin family signature 1. / Outer membrane adhesin/peptidase omptin
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsJiang, L.Y. / Ran, T.T. / Gao, S. / Wang, W.W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972711 China
National Natural Science Foundation of China (NSFC)31672553 China
CitationJournal: To Be Published
Title: Crystal structure of pOmpT
Authors: Liu, J.H. / Ran, T.T. / Jiang, L.Y. / Wang, W.W. / Gao, S.
History
DepositionMay 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OmpT
B: OmpT


Theoretical massNumber of molelcules
Total (without water)67,4582
Polymers67,4582
Non-polymers00
Water181
1
A: OmpT


Theoretical massNumber of molelcules
Total (without water)33,7291
Polymers33,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OmpT


Theoretical massNumber of molelcules
Total (without water)33,7291
Polymers33,7291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.765, 93.765, 150.344
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein OmpT / Omptin / Omptin family outer membrane protease / Outer membrane / Outer membrane protease / Outer ...Omptin / Omptin family outer membrane protease / Outer membrane / Outer membrane protease / Outer membrane protease (Omptin) / Outer membrane protease VII / Protease / Protease 7 / Protease VII (Omptin)


Mass: 33729.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3L7I1, omptin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.95→19.89 Å / Num. obs: 16591 / % possible obs: 99.6 % / Observed criterion σ(I): 1.3 / Redundancy: 19.8 % / CC1/2: 0.999 / Rpim(I) all: 0.038 / Rrim(I) all: 0.17 / Net I/σ(I): 13.4
Reflection shellResolution: 2.95→3.13 Å / Num. unique obs: 2635 / CC1/2: 0.586 / Rpim(I) all: 0.634

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Processing

Software
NameVersionClassification
PHENIXV1.6refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1i78

1i78


Resolution: 2.95→19.6 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3237 --
Rwork0.3052 --
obs-16533 99.3 %
Displacement parametersBiso mean: 95.09 Å2
Refinement stepCycle: LAST / Resolution: 2.95→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4214 0 0 1 4215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01174337
X-RAY DIFFRACTIONf_angle_d1.74265880
X-RAY DIFFRACTIONf_chiral_restr0.1354583
X-RAY DIFFRACTIONf_plane_restr0.0051761
X-RAY DIFFRACTIONf_dihedral_angle_d13.68292464

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