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- PDB-4ctd: X-ray structure of an engineered OmpG loop6-deletion -

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Basic information

Entry
Database: PDB / ID: 4ctd
TitleX-ray structure of an engineered OmpG loop6-deletion
ComponentsOUTER MEMBRANE PROTEIN G
KeywordsTRANSPORT PROTEIN / ION-CHANNEL-ENGINEERING / PORIN
Function / homology
Function and homology information


carbohydrate transmembrane transport / oligosaccharide transporting porin activity / maltose transporting porin activity / porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Outer membrane porin G / Outer membrane protein G (OmpG) / monomeric porin ompg / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane porin G
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGrosse, W. / Essen, L.-O.
CitationJournal: Biochemistry / Year: 2014
Title: Structure-Based Engineering of a Minimal Porin Reveals Loop- Independent Channel Closure.
Authors: Grosse, W. / Psakis, G. / Mertins, B. / Reiss, P. / Windisch, D. / Brademann, F. / Burck, J. / Ulrich, A. / Koert, U. / Essen, L.
History
DepositionMar 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Aug 9, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Dec 20, 2023Group: 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 / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _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 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-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: OUTER MEMBRANE PROTEIN G
B: OUTER MEMBRANE PROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,53818
Polymers63,8872
Non-polymers1,65116
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-109.8 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.940, 60.060, 59.760
Angle α, β, γ (deg.)70.45, 95.24, 70.58
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 3:19 OR RESSEQ 27:55 OR RESSEQ...
211CHAIN B AND (RESSEQ 3:19 OR RESSEQ 27:55 OR RESSEQ...

NCS oper: (Code: given
Matrix: (-0.33501, -0.94221, -0.00413), (-0.94221, 0.33499, 0.00493), (-0.00326, 0.00554, -0.99998)
Vector: -0.67539, -0.35593, 0.62469)

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Components

#1: Protein OUTER MEMBRANE PROTEIN G


Mass: 31943.514 Da / Num. of mol.: 2 / Fragment: MATURE PROTEIN WITHOUT PELB LEADER SEQUENCE / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DELETION OF FLEXIBLE LOOP6 WITH OPTIMIZED B-TURN / Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): OMP9 / References: UniProt: P76045
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
Sequence detailsENGINEERED W217A SUBSTITUTION, ENGINEERED DELETION OF 218- 229 (S, N, W, D, W, Q, D, D, I, E, R, E) ...ENGINEERED W217A SUBSTITUTION, ENGINEERED DELETION OF 218- 229 (S, N, W, D, W, Q, D, D, I, E, R, E), C-TERMINAL HIS- TAG

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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: 2.92 Å3/Da / Density % sol: 57.9 %
Description: DATA WERE SCALED BY DIFFRACTION ANISOTROPY SERVER, MBI UCLA, DA 39.82, DB -15.04, DC -24.78, ENGINEERED W217A SUBSTITUTION AND ENGINEERED DELETION OF S218 TO E229 AND C209Y MUTATION WERE ...Description: DATA WERE SCALED BY DIFFRACTION ANISOTROPY SERVER, MBI UCLA, DA 39.82, DB -15.04, DC -24.78, ENGINEERED W217A SUBSTITUTION AND ENGINEERED DELETION OF S218 TO E229 AND C209Y MUTATION WERE APPLIED TO 2WVP BEFORE USE IN MR
Crystal growpH: 8.5
Details: 0.1 M TRIS/HCL, PH 8.5, 20% (V/V) ETOH; 8 MG/ML OMPG IN 20 MM TRIS/HCL, PH 8.0, 250 MM NACL, 10% (V/V) GLYCEROL, 0.4% (V/V) C8E4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3.2→44.21 Å / Num. obs: 11053 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 5.3
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WVP

2wvp


Resolution: 3.2→44.21 Å / SU ML: 0.41 / σ(F): 1.98 / Phase error: 29.77 / Stereochemistry target values: ML
Details: COORDINATES WERE REFINED AGAINST DATA SCALED BY DIFFRACTION ANISOTROPY SERVER, MBI UCLA, DA 39.82, DB -15.04, DC -24.78
RfactorNum. reflection% reflection
Rfree0.2889 529 4.9 %
Rwork0.2384 --
obs0.2409 10858 91.24 %
Solvent computationShrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.289 Å2 / ksol: 0.315 e/Å3
Displacement parametersBiso mean: 17.81 Å2
Baniso -1Baniso -2Baniso -3
1--14.8237 Å2-1.3382 Å2-2.271 Å2
2---17.5048 Å2-2.4536 Å2
3----30.8037 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 74 0 3848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154174
X-RAY DIFFRACTIONf_angle_d1.3115337
X-RAY DIFFRACTIONf_dihedral_angle_d19.1931351
X-RAY DIFFRACTIONf_chiral_restr0.092527
X-RAY DIFFRACTIONf_plane_restr0.007688
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1829X-RAY DIFFRACTIONPOSITIONAL
12B1829X-RAY DIFFRACTIONPOSITIONAL0.038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.5220.29751320.25252500X-RAY DIFFRACTION88
3.522-4.03140.32651370.25122652X-RAY DIFFRACTION94
4.0314-5.07790.27121350.20542600X-RAY DIFFRACTION93
5.0779-44.21450.26261250.25472577X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3171-0.01140.13081.04630.09440.88810.0364-0.06410.44350.07420.0250.2993-0.3257-0.0382-0.16240.1049-0.00780.05050.14710.03630.2445-9.5971-12.74723.2958
20.3929-0.02110.14370.1134-0.10340.1740.087-0.0193-0.15130.00870.05660.137-0.0062-0.07010.73220.07980.0351-0.0280.102-0.05160.43990.3624-17.39636.7659
30.7608-0.2995-0.14891.3165-0.42550.96530.3131-0.0094-0.1872-0.00210.12610.4658-0.0004-0.01841.39370.14850.0353-0.06020.02470.11060.1468-9.2887-26.97943.4926
40.74550.0615-0.05870.42820.10620.45650.2210.03920.084-0.16760.185-0.00410.0279-0.20820.5231-0.075-0.09160.02910.09420.11630.202214.30724.1466-2.2185
51.09670.3017-0.59750.8235-0.25390.51750.05530.21930.1342-0.22660.2270.039-0.1531-0.19010.54770.34810.044-0.08940.1526-0.05340.249415.5673-6.5041-6.2274
62.30550.2632-0.1221.3574-0.33260.593-0.00810.38590.317-0.23270.0259-0.0091-0.0879-0.1026-0.01190.13960.0516-0.040.022-0.1610.225227.836-0.6212-2.8919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 3:137)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 138:160)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 161:270)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 3:137)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 138:160)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 161:270)

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