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- PDB-9oq7: Chlamydia muridarum Major Outer Membrane Protein -

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Basic information

Entry
Database: PDB / ID: 9oq7
TitleChlamydia muridarum Major Outer Membrane Protein
ComponentsMajor outer membrane porin
KeywordsMEMBRANE PROTEIN / Chlamydia muridarum Major Outer Membrane Protein / Porin / Chlamydia vaccine candidate / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane / regulation of cell shape / structural molecule activity
Similarity search - Function
Major outer membrane protein, Chlamydia / Chlamydia major outer membrane protein
Similarity search - Domain/homology
LAURIC ACID / sphingomyelin / 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Major outer membrane porin
Similarity search - Component
Biological speciesChlamydia muridarum (agent of mouse pneumonitis)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsGuo, Y. / Borek, D. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Chlamydia muridarum Major Outer Membrane Protein
Authors: Guo, Y. / Borek, D.
History
DepositionMay 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major outer membrane porin
B: Major outer membrane porin
G: Major outer membrane porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,31821
Polymers119,3693
Non-polymers5,94918
Water64936
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.5, -0.866025), (0.866025, -0.5), (1)459.52939, 123.1306
3given(-0.5, 0.866025), (-0.866025, -0.5), (1)123.13061, 459.52939

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Components

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Protein / Sugars , 2 types, 6 molecules ABG

#1: Protein Major outer membrane porin / MOMP


Mass: 39789.793 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Chlamydia muridarum (agent of mouse pneumonitis)
References: UniProt: P75024
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 51 molecules

#2: Chemical ChemComp-PEX / 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 522.632 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H49NO8P
#3: Chemical
ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H24O2
#5: Chemical ChemComp-FO4 / sphingomyelin


Mass: 814.233 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C47H94N2O6P
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chlamydia muridarum Major Outer Membrane Protein / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Chlamydia muridarum (agent of mouse pneumonitis)
Buffer solutionpH: 5.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87699 / Symmetry type: POINT
RefinementResolution: 2.96→114.37 Å / Cor.coef. Fo:Fc: 0.85 / SU B: 16.174 / SU ML: 0.284 / ESU R: 0.268
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.39444 --
obs0.39444 68820 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 43.632 Å2
Refinement stepCycle: 1 / Total: 3002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.010.0133075
ELECTRON MICROSCOPYr_bond_other_d0.0330.0152907
ELECTRON MICROSCOPYr_angle_refined_deg1.3731.6754144
ELECTRON MICROSCOPYr_angle_other_deg1.4691.6336723
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.395376
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.29123.05141
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.78815462
ELECTRON MICROSCOPYr_dihedral_angle_4_deg9.2651514
ELECTRON MICROSCOPYr_chiral_restr0.0720.2404
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.023424
ELECTRON MICROSCOPYr_gen_planes_other0.0020.02687
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it0.6394.5041497
ELECTRON MICROSCOPYr_mcbond_other0.6414.5091488
ELECTRON MICROSCOPYr_mcangle_it1.226.7631870
ELECTRON MICROSCOPYr_mcangle_other1.226.7631871
ELECTRON MICROSCOPYr_scbond_it0.3884.8321578
ELECTRON MICROSCOPYr_scbond_other0.3884.8391574
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other0.777.1882275
ELECTRON MICROSCOPYr_long_range_B_refined3.07910722
ELECTRON MICROSCOPYr_long_range_B_other3.07910722
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.96→3.037 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.892 5107 -
obs--100 %

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