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- PDB-5ek5: STRUCTURAL CHARACTERIZATION OF IRMA FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 5ek5
TitleSTRUCTURAL CHARACTERIZATION OF IRMA FROM ESCHERICHIA COLI
ComponentsIRMA
KeywordsUNKNOWN FUNCTION / FIBRONECTIN FOLD / VIRULENCE / SECRETED PROTEIN
Function / homologyInterleukin receptor mimic protein A / interleukin receptor mimic protein A / FORMIC ACID / Aec69 / IrmA family protein
Function and homology information
Biological speciesEscherichia coli CFT073 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.26 Å
AuthorsHeras, B. / Moriel, D.G. / Paxman, J.J. / Schembri, M.A.
CitationJournal: Mbio / Year: 2016
Title: Molecular and Structural Characterization of a Novel Escherichia coli Interleukin Receptor Mimic Protein.
Authors: Moriel, D.G. / Heras, B. / Paxman, J.J. / Lo, A.W. / Tan, L. / Sullivan, M.J. / Dando, S.J. / Beatson, S.A. / Ulett, G.C. / Schembri, M.A.
History
DepositionNov 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IRMA
B: IRMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9066
Polymers28,7402
Non-polymers1674
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-12 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.999, 93.999, 93.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-201-

CL

21B-201-

NA

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein IRMA


Mass: 14369.842 Da / Num. of mol.: 2 / Fragment: UNP residues 25-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli CFT073 (bacteria) / Strain: CFT073
Gene: ACM20_11530, HUS2011_3591, SK67_04736, SK69_02333, SK70_03200, SK71_02973, SK75_00406, SK76_00877, SK83_00395, SK84_04099, SK86_02365, SY51_17055
Plasmid: PMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: Q6KD75, UniProt: A0A0H2VAX3*PLUS

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Non-polymers , 5 types, 120 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 MM BIS-TRIS PROPANE PH 9.0 AND 2% (W/V) POLYETHYLENE GLYCOL (PEG) 2000, VAPOR DIFFUSION, TEMPERATURE 294K
PH range: 9

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E SUPERBRIGHT11.5418
SYNCHROTRONAustralian Synchrotron MX220.9686
Detector
TypeIDDetectorDateDetails
RIGAKU SATURN 9441CCDJul 17, 2012MIRRORS
ADSC QUANTUM 210r2CCDAug 24, 2012MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTALSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.96861
ReflectionResolution: 2.26→47 Å / Num. obs: 13278 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 21.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 37.1
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
HKL-2000data reduction
HKL-2000data scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.26→47 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1873 14.13 %Random selection
Rwork0.215 ---
obs0.222 13251 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.25 Å2
Refinement stepCycle: LAST / Resolution: 2.26→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 9 116 1989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051905
X-RAY DIFFRACTIONf_angle_d1.092584
X-RAY DIFFRACTIONf_dihedral_angle_d13.195694
X-RAY DIFFRACTIONf_chiral_restr0.043298
X-RAY DIFFRACTIONf_plane_restr0.004339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.31970.36431560.3215820X-RAY DIFFRACTION100
2.3197-2.3880.30711270.2773896X-RAY DIFFRACTION100
2.388-2.4650.31161600.27826X-RAY DIFFRACTION100
2.465-2.55310.31841480.2626874X-RAY DIFFRACTION100
2.5531-2.65540.29131230.2507878X-RAY DIFFRACTION100
2.6554-2.77620.30731410.2761873X-RAY DIFFRACTION100
2.7762-2.92250.32071400.2553871X-RAY DIFFRACTION100
2.9225-3.10560.32081410.2426874X-RAY DIFFRACTION100
3.1056-3.34530.28321530.2313868X-RAY DIFFRACTION100
3.3453-3.68190.25461300.2059889X-RAY DIFFRACTION100
3.6819-4.21440.2181510.1747877X-RAY DIFFRACTION100
4.2144-5.30850.19241240.1503926X-RAY DIFFRACTION100
5.3085-47.00970.24381790.2206906X-RAY DIFFRACTION100
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)
16.43223.010.72735.977-1.13137.1938-0.2075-0.69120.2380.51090.09940.0869-0.27560.38070.13420.327-0.07450.00870.24050.00730.104731.7722-2.75089.9593
26.7521.6251-2.66183.603-0.20072.4274-0.20310.33260.00250.11560.09560.51330.3818-0.41860.14390.336-0.05880.01740.41530.00330.23519.6229-8.28185.7384
32.0282-2.12282.02647.48750.24716.85540.18450.08570.3401-0.18640.01440.0470.47020.1105-0.01960.303-0.08790.03510.22180.05720.208735.961-1.14936.7788
49.7188-7.6369-0.98855.99830.77780.10110.60741.3118-0.4759-1.2042-0.73240.0888-0.1346-0.46080.15960.4686-0.1139-0.10850.78640.09560.636613.2599-0.49739.1716
53.6596-1.9773-3.76582.12872.37466.4999-0.17920.0543-0.29270.15740.1143-0.04150.7733-0.21480.1540.3864-0.0659-0.00870.24510.03180.294629.8973-9.846610.1524
67.30491.2208-2.57552.0997-1.75956.9575-0.2955-0.13540.18790.01570.03110.03780.24990.96760.19310.40070.0291-0.01960.5637-0.01190.221729.5172-1.570630.682
75.9829-8.8614-5.3561.98997.93414.79151.4876-1.61181.3741-1.3437-0.2933-1.2375-1.89460.693-1.16090.3122-0.27140.14141.2987-0.30740.775643.89238.165827.3985
82.32810.345-1.89473.88750.06574.19220.0225-0.56680.34660.5233-0.16690.1467-0.91280.46990.12920.5145-0.0371-0.02860.4341-0.0850.268721.93815.633336.0015
93.76950.9171-0.00468.1428-0.98126.957-0.1081-0.6479-0.35950.27160.0931-1.0567-0.25581.72720.15920.51150.0358-0.04710.79690.05720.452837.6552-0.13131.9048
102.875-1.1807-0.2826.63792.84377.1143-0.1892-0.36450.64350.21710.3536-0.548-1.0530.5424-0.12870.4007-0.0857-0.03260.4430.01790.383128.8575.950229.4509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 90 )
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 125 )
6X-RAY DIFFRACTION6chain 'B' and (resid 8 through 33 )
7X-RAY DIFFRACTION7chain 'B' and (resid 34 through 43 )
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 65 )
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 84 )
10X-RAY DIFFRACTION10chain 'B' and (resid 85 through 127 )

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