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- PDB-5g26: Unveiling the Mechanism Behind the in-meso Crystallization of Mem... -

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Basic information

Entry
Database: PDB / ID: 5g26
TitleUnveiling the Mechanism Behind the in-meso Crystallization of Membrane Proteins
ComponentsINTIMIN
KeywordsMEMBRANE PROTEIN / LYOTROPIC LIQUID CRYSTALLINE SYSTEMS / IN MESO CRYSTALLISATION
Function / homology
Function and homology information


cell outer membrane / cell adhesion
Similarity search - Function
Inverse autotransporter, beta-domain / Intimin, C-terminal / Intimin C-type lectin domain / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily / : / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Bacterial Ig-like domain (group 1) ...Inverse autotransporter, beta-domain / Intimin, C-terminal / Intimin C-type lectin domain / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily / : / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2 / Lysin motif / LysM domain / LysM domain profile. / LysM domain / Porin / C-type lectin-like/link domain superfamily / C-type lectin fold / Immunoglobulin-like fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate / (2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate / Intimin / Intimin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsZabara, A. / Newman, J. / Peat, T.S.
CitationJournal: Nanoscale / Year: 2017
Title: The Nanoscience Behind the Art of in-Meso Crystallization of Membrane Proteins.
Authors: Zabara, A. / Meikle, T.G. / Newman, J. / Peat, T.S. / Conn, C.E. / Drummond, C.J.
History
DepositionApr 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTIMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1015
Polymers27,7871
Non-polymers1,3144
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.944, 119.925, 39.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2018-

HOH

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Components

#1: Protein INTIMIN


Mass: 27786.594 Da / Num. of mol.: 1 / Fragment: MEMBRANE DOMAIN, UNP RESIDUES 197-438
Source method: isolated from a genetically manipulated source
Details: MISSING N-TERMINAL DOMAIN / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O157 / Plasmid: PET9B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0LBN7, UniProt: P43261*PLUS
#2: Chemical ChemComp-97N / (2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate


Mass: 328.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H36O4
#3: Chemical ChemComp-97M / (2R)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate


Mass: 328.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H36O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMONOPALMITOLEIN (LIG): LIPID
Sequence detailsN- AND C-TERMINAL CYTOPLASMIC DOMAINS DELETED

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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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 4.3
Details: 100MM TRISODIUM CITRATE/CITRIC ACID PH 4.3, 113MM NACL, 78MM MGCL2, 27% PEG 400 (V/V); MONOPALMITOLEIN USED FOR IN-MESO CRYSTALLISATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.42→41.7 Å / Num. obs: 10728 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.3
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.9 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E1S

4e1s


Resolution: 2.42→41.5 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.875 / SU B: 12.8 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 0.589 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REFINED INDIVIDUALLY THERE IS EXTRA POSITIVE (WEAK) DENSITY FOR MORE LIPIDS BUT THESE WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27844 523 4.9 %RANDOM
Rwork0.22186 ---
obs0.22448 10166 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.743 Å2
Baniso -1Baniso -2Baniso -3
1-8.23 Å20 Å20 Å2
2---2.58 Å20 Å2
3----5.65 Å2
Refinement stepCycle: LAST / Resolution: 2.42→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 92 33 2079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192108
X-RAY DIFFRACTIONr_bond_other_d0.0030.021916
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9662830
X-RAY DIFFRACTIONr_angle_other_deg0.96134403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4785242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.06224.017117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95215306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4861513
X-RAY DIFFRACTIONr_chiral_restr0.0870.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02557
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.344.985968
X-RAY DIFFRACTIONr_mcbond_other3.3384.985967
X-RAY DIFFRACTIONr_mcangle_it4.8248.3911210
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3955.8081140
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 42 -
Rwork0.322 650 -
obs--88.83 %

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