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- PDB-2xe5: Molecular insights into clinically isolated OmpC mutants and thei... -

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Entry
Database: PDB / ID: 2xe5
TitleMolecular insights into clinically isolated OmpC mutants and their role in multi-drug resistance (OmpC26)
ComponentsOUTER MEMBRANE PORIN C
KeywordsTRANSPORT PROTEIN / CELL MEMBRANE / ION TRANSPORT / PORIN
Function / homology
Function and homology information


porin activity / pore complex / ion transport / cell outer membrane
Porin, Gram-negative type / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / Porin domain superfamily / Porin domain, Gram-negative type / Gram-negative porin / General diffusion Gram-negative porins signature.
Membrane protein
Specimen sourceESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBamford, V.A. / Naismith, J.H.
CitationJournal: Plos One / Year: 2011
Title: Altered Antibiotic Transport in Ompc Mutants Isolated from a Series of Clinical Strains of Multi-Drug Resistant E. Coli.
Authors: Lou, H. / Chen, M. / Black, S.S. / Bushell, S.R. / Ceccarelli, M. / Mach, T. / Beis, K. / Low, A.S. / Bamford, V.A. / Booth, I.R. / Bayley, H. / Naismith, J.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 11, 2010 / Release: May 26, 2010
RevisionDateData content typeGroupProviderType
1.0May 26, 2010Structure modelrepositoryInitial release
1.1Nov 16, 2011Structure modelDatabase references / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OUTER MEMBRANE PORIN C
B: OUTER MEMBRANE PORIN C
C: OUTER MEMBRANE PORIN C
D: OUTER MEMBRANE PORIN C
E: OUTER MEMBRANE PORIN C
F: OUTER MEMBRANE PORIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,01953
Polyers229,7776
Non-polymers6,24247
Water7,062392
1
D: OUTER MEMBRANE PORIN C
E: OUTER MEMBRANE PORIN C
F: OUTER MEMBRANE PORIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,20120
Polyers114,8893
Non-polymers2,31217
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14380 Å2
ΔGint-62.8 kcal/mol
Surface area42290 Å2
MethodPISA
2
A: OUTER MEMBRANE PORIN C
B: OUTER MEMBRANE PORIN C
C: OUTER MEMBRANE PORIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,81933
Polyers114,8893
Non-polymers3,93030
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15800 Å2
ΔGint-30.4 kcal/mol
Surface area43270 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)74.180, 93.680, 115.910
Angle α, β, γ (deg.)98.74, 108.79, 109.71
Int Tables number1
Space group name H-MP1

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Components

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Protein/peptide , 1 types, 6 molecules ABCDEF

#1: Protein/peptide
OUTER MEMBRANE PORIN C / OUTER MEMBRANE PROTEIN C / OMPC


Mass: 38296.230 Da / Num. of mol.: 6 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O6 / Description: OMPC26 ISOLATED FROM CLINICAL MUTANTS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9K597

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Non-polymers , 10 types, 439 molecules

#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Formula: C16H34O5 / Comment: C8E (detergent) *YM
#3: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 10 / Formula: C6H14 / Hexane
#4: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 6 / Formula: C12H26 / Dodecane
#5: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 10 / Formula: C8H18 / Octane
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Formula: SO4 / Sulfate
#7: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 6 / Formula: C10H22 / Decane
#8: Chemical ChemComp-ASZ / 2-(DIMETHYLAMINO)ETHANESULFONIC ACID


Mass: 153.200 Da / Num. of mol.: 1 / Formula: C4H11NO3S
#9: Chemical ChemComp-OES / N-OCTYL-2-HYDROXYETHYL SULFOXIDE


Mass: 206.345 Da / Num. of mol.: 2 / Formula: C10H22O2S
#10: Chemical ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 3 / Formula: C7H16 / Heptane
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Formula: H2O / Water

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Details

Sequence detailsTHIS IS FROM A CLINICAL SEQUENCE DESCRIBED IN PUBMED ID: 11722730. A.S.LOW,F.M.MACKENZIE,I.M.GOULD, ...THIS IS FROM A CLINICAL SEQUENCE DESCRIBED IN PUBMED ID: 11722730. A.S.LOW,F.M.MACKENZIE,I.M.GOULD, I.R.BOOTH. PROTECTED ENVIRONMENTS ALLOW PARALLEL EVOLUTION OF A BACTERIAL PATHOGEN IN A PATIENT SUBJECTED TO LONG-TERM ANTIBIOTIC THERAPY. MOL.MICROBIOL. 42,619

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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: 2.99 Å3/Da / Density % sol: 58.8 %
Description: DATA WERE TRUNCATED USING WEBSERVER STRONG ET AL., 2006, PROC NATL ACAD SCI U S A, 103, 8060-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.28→79 Å / Num. obs: 118130 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.8 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.6.0060refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XE1
Resolution: 2.28→29.41 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.875 / SU B: 15.665 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.491 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS USED REFMAC V5.6 WHICH HAS LOCAL NCS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26707 4815 5 %RANDOM
Rwork0.22605 ---
obs0.22804 95882 79.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0.05 Å20 Å2
2---0.13 Å2-0.21 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.28→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16260 0 420 392 17072
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0110.02116999
r_bond_other_d0.0010.0211415
r_angle_refined_deg1.3611.93922856
r_angle_other_deg2.944327564
r_dihedral_angle_1_deg6.20352052
r_dihedral_angle_2_deg36.29925960
r_dihedral_angle_3_deg13.479152520
r_dihedral_angle_4_deg13.4461578
r_chiral_restr0.0780.22254
r_gen_planes_refined0.0050.0219542
r_gen_planes_other0.0050.023762
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 50 -
Rwork0.238 789 -
obs--9.41 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.6402-1.287-1.79834.18555.03756.1247-0.16160.61440.3197-0.11820.00460.202-0.0518-0.16450.1570.3397-0.1126-0.08680.57360.27220.1456-10.683.757-9.487
22.73670.0006-0.79740.77450.2320.5749-0.10280.6557-0.03380.0541-0.03410.05880.1305-0.2150.13690.2219-0.104-0.03090.49170.09120.0943-19.082-5.904-6.592
32.60270.37110.04092.1327-0.00051.7951-0.06280.26990.03590.05560.01460.22320.231-0.32690.04820.0777-0.04370.02260.35570.04920.0724-27.583-4.4631.798
41.95430.7984-0.00572.2735-0.57081.94860.02180.31760.54640.3206-0.00690.3229-0.4034-0.1961-0.01490.1780.0553-0.04590.34850.13810.2475-25.68110.3266.481
56.8681-1.36752.82851.933-1.29912.6173-0.19370.84450.40540.01480.1269-0.0737-0.2640.09260.06680.2941-0.09980.0040.36640.13860.10246.9779.84-8.051
63.2791-0.31440.24621.60080.47050.6757-0.1590.35190.94820.03550.1235-0.0448-0.21930.04560.03550.2913-0.0504-0.03810.25810.14590.35293.4120.522-1.298
75.8419-0.51820.031.845-0.67192.2645-0.2092-0.08091.45610.20360.1912-0.1235-0.1987-0.07270.0180.4079-0.0823-0.11380.0886-0.10340.63049.9724.7197.961
83.69320.3877-0.183.2761.52786.3938-0.1215-0.29620.67620.24520.0101-0.3134-0.34480.50360.11140.1572-0.0255-0.07530.12010.01120.358922.18615.1718.348
93.80312.9282-2.06493.8667-1.692.0975-0.21030.6845-0.2707-0.3071-0.082-0.13770.0410.07340.29220.2861-0.0651-0.01630.538-0.00040.10283.634-8.233-11.524
101.86090.33130.4472.12470.06891.4074-0.30030.5566-0.2833-0.12310.1384-0.25930.10020.19550.16190.2052-0.07740.02620.3358-0.04130.172315.544-11.942-7.164
112.3510.2264-0.00261.7148-0.2511.9822-0.18780.2508-0.55560.07720.0022-0.15420.20930.13770.18560.2219-0.02250.07140.3048-0.05360.271917.099-21.966-0.734
122.6699-0.39080.66041.7591-0.25772.4775-0.09650.2379-0.7210.04610.03790.06540.49570.18450.05850.3276-0.12380.11020.1955-0.16260.35442.831-28.239-0.228
133.9971-2.28981.96553.6393-2.00281.814-0.1027-0.85890.15040.29760.0021-0.0171-0.0474-0.1450.10060.27530.07350.01380.493-0.06820.0701-33.589-13.89960.097
142.1769-0.3011-0.62891.9929-0.02581.4667-0.1627-0.55660.28270.14590.0711-0.3135-0.08570.17490.09150.18970.0648-0.03710.3075-0.01990.1158-21.685-10.19955.769
152.7161-0.1415-0.05161.69180.39392.0511-0.1756-0.26180.5806-0.01820.0241-0.1256-0.18120.19570.15150.2441-0.0027-0.08210.2271-0.06360.2459-20.153-0.20849.3
163.60560.6642-1.06722.1715-1.17693.0718-0.0769-0.26740.8482-0.13840.1230.2156-0.27860.0661-0.0460.32140.0759-0.10930.1708-0.1920.3827-34.4026.02948.728
172.30031.51011.88533.77764.47525.5908-0.1735-0.5698-0.2550.0135-0.02930.2069-0.128-0.24850.20280.29910.00980.01390.54040.20620.1089-47.917-25.87558.118
183.0538-0.09150.8360.95080.16810.3121-0.183-0.64350.08520.01860.07340.0835-0.035-0.18630.10950.23340.07250.00320.50480.06040.1264-56.311-16.29955.154
192.52070.0343-0.00991.6724-0.04761.3418-0.1512-0.2620.1079-0.04110.12740.1889-0.1-0.18730.02380.14650.0797-0.01570.37520.0780.0551-64.76-17.78346.738
201.8537-0.3820.43761.841-0.79792.0701-0.0662-0.2206-0.3697-0.16540.05560.18680.05-0.24450.01060.2006-0.05970.04070.3330.13030.2027-62.806-32.5742.108
214.98161.2057-1.92582.0008-1.43532.3756-0.147-0.4559-0.40150.04750.1861-0.1380.2538-0.2726-0.03910.2760.0268-0.02610.39650.14350.1098-30.176-31.98656.728
222.30160.622-0.40931.53910.45831.1026-0.2743-0.1895-0.7111-0.10030.13-0.13420.3070.05540.14430.29170.01210.04940.22090.10490.2994-33.702-42.71150.056
234.23840.323-0.10042.2317-0.13211.7005-0.15850.1475-0.939-0.25410.0208-0.20570.31980.04080.13770.36810.02860.17170.0196-0.06840.4774-27.128-46.99840.824
243.95340.7513-0.2862.81821.16764.3902-0.38580.1446-0.7011-0.3580.1594-0.39530.18520.63730.22640.30140.05170.09650.11020.02460.421-14.931-37.44440.337
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDAuth asym-IDAuth seq-ID
11A1 - 50
22A51 - 150
33A151 - 275
44A276 - 343
55B1 - 50
66B51 - 150
77B151 - 275
88B276 - 343
99C1 - 50
1010C51 - 150
1111C151 - 275
1212C276 - 343
1313D1 - 50
1414D51 - 150
1515D151 - 275
1616D276 - 343
1717E1 - 50
1818E51 - 150
1919E151 - 275
2020E276 - 343
2121F1 - 50
2222F51 - 150
2323F151 - 275
2424F276 - 343

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