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- PDB-5jcr: Crystal structure of the FimH lectin domain from E.coli K12 in co... -

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Basic information

Entry
Database: PDB / ID: 5jcr
TitleCrystal structure of the FimH lectin domain from E.coli K12 in complex with methyl alpha-D-mannopyrannoside in spacegroup P212121
ComponentsProtein FimH
KeywordsSUGAR BINDING PROTEIN / type 1 pilus / FimH / UTI / bladder infection / lectin / mannose / carbohydrate
Function / homology
Function and homology information


pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / cell adhesion
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
methyl alpha-D-mannopyranoside / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsJakob, R.P. / Rabbani, S. / Ernst, B. / Maier, T.
CitationJournal: To Be Published
Title: Crystal structure of the FimH lectin domain from E.coli K12 in complex with methyl alpha-D-mannopyrannoside in spacegroup P212121
Authors: Jakob, R.P. / Rabbani, S. / Ernst, B. / Maier, T.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein FimH
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2224
Polymers33,8342
Non-polymers3882
Water12,322684
1
A: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1112
Polymers16,9171
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1112
Polymers16,9171
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.980, 68.950, 95.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein FimH


Mass: 16916.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fimH, b4320, JW4283 / Plasmid: pTRC99a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08191
#2: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / Source method: isolated from a natural source / Formula: H2O

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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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammoniumsulfat, 30% PEG3350, 0.1 M Hepes 7.0, frozen by addition of 20 % EG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.701→55.923 Å / Num. obs: 45971 / % possible obs: 98.9 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.3
Reflection shellResolution: 1.701→1.8 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X50

4x50


Resolution: 1.701→55.923 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.93
RfactorNum. reflection% reflection
Rfree0.2298 2232 4.86 %
Rwork0.2094 --
obs0.2104 45971 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.701→55.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 26 684 3102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042488
X-RAY DIFFRACTIONf_angle_d1.0933421
X-RAY DIFFRACTIONf_dihedral_angle_d10.736861
X-RAY DIFFRACTIONf_chiral_restr0.039406
X-RAY DIFFRACTIONf_plane_restr0.005440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.701-1.7380.26651360.25772679X-RAY DIFFRACTION98
1.738-1.77840.25381250.22982706X-RAY DIFFRACTION99
1.7784-1.82290.22211380.22172701X-RAY DIFFRACTION99
1.8229-1.87220.28881460.24012702X-RAY DIFFRACTION99
1.8722-1.92730.29981420.28142652X-RAY DIFFRACTION98
1.9273-1.98950.27431230.22432736X-RAY DIFFRACTION99
1.9895-2.06060.21761330.19822707X-RAY DIFFRACTION100
2.0606-2.14310.22311460.19072732X-RAY DIFFRACTION100
2.1431-2.24070.27641300.24732682X-RAY DIFFRACTION97
2.2407-2.35880.23841290.22772671X-RAY DIFFRACTION97
2.3588-2.50660.21911420.19352741X-RAY DIFFRACTION100
2.5066-2.70010.2011380.22746X-RAY DIFFRACTION100
2.7001-2.97180.24121210.19382804X-RAY DIFFRACTION100
2.9718-3.40180.19561560.19192763X-RAY DIFFRACTION100
3.4018-4.28570.21521580.19672788X-RAY DIFFRACTION99
4.2857-55.95280.22321690.19582929X-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)
11.41760.304-0.04872.25771.82923.43780.0135-0.03440.20430.170.0697-0.0127-0.25180.1117-0.00380.1880.03210.03410.15570.00790.1438-14.30510.1688-2.5822
20.41270.0970.12910.89570.35511.9687-0.00550.0052-0.01230.0362-0.0656-0.043-0.15630.00220.08420.12770.01440.00510.14080.00750.1334-14.1549-0.907618.228
30.2607-0.12140.21930.4308-0.38032.4803-0.01580.0280.02330.03830.0624-0.0441-0.0904-0.082-0.03040.1310.0175-0.00660.0950.00370.1202-22.8126-1.21950.2806
43.1348-0.2564.47270.5326-0.26996.48340.19810.2868-0.246-0.03920.0275-0.02930.34610.3551-0.23730.12280.0214-0.00030.1117-0.00660.0973-18.708-12.34144.0092
51.47290.6151.27990.62440.2183.69880.0986-0.1007-0.0682-0.1158-0.1138-0.09330.1234-0.04230.05550.11880.0139-0.01820.07590.0030.1159-17.7331-10.630318.4201
60.581-0.62440.28121.7639-1.74772.1869-0.012-0.0029-0.0842-0.02660.17380.04430.126-0.269-0.20550.12640.0002-0.01180.1128-0.00030.1242-25.2758-12.88566.9718
70.3236-0.26870.69050.4294-0.95442.4585-0.0230.00040.00820.12190.05110.058-0.1965-0.0854-0.11260.11110.0151-0.00050.0999-0.00060.1122-21.9985-4.281310.8186
81.83371.3323-2.11551.7192-1.80892.6404-0.03940.0192-0.02410.09880.1136-0.30560.00060.6152-0.01630.1414-0.0007-0.01740.141-0.00970.1271-6.7465-3.459322.9746
90.3817-0.04630.24580.5811-0.23251.43880.06340.1099-0.0331-0.0375-0.0179-0.03660.12460.2135-0.06130.10680.02490.0110.1083-0.01190.1126-14.9851-7.55975.3941
100.20860.0175-0.23460.1097-0.03881.59570.0640.0012-0.04510.07270.01390.0740.2773-0.0686-0.0940.132-0.0550.00450.10540.00460.1289-47.21340.720217.2143
110.31860.0395-0.67620.64280.62682.40870.04230.03030.01270.01030.0369-0.0304-0.0597-0.0138-0.09980.066-0.0383-0.00310.1098-0.00610.0914-42.63527.555310.7163
120.2513-0.4924-0.4370.99741.07581.67870.0189-0.05170.0173-0.10960.1588-0.2413-0.140.3892-0.09830.0961-0.03390.02430.1529-0.03230.1317-37.64338.156710.3107
130.2109-0.00210.10420.26490.07891.47620.0499-0.02380.0150.01060.03090.0237-0.1407-0.1133-0.08060.1074-0.03110.00570.09660.00350.1042-48.19297.278417.4974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 64 )
5X-RAY DIFFRACTION5chain 'A' and (resid 65 through 77 )
6X-RAY DIFFRACTION6chain 'A' and (resid 78 through 95 )
7X-RAY DIFFRACTION7chain 'A' and (resid 96 through 116 )
8X-RAY DIFFRACTION8chain 'A' and (resid 117 through 124 )
9X-RAY DIFFRACTION9chain 'A' and (resid 125 through 158 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 40 )
11X-RAY DIFFRACTION11chain 'B' and (resid 41 through 77 )
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 104 )
13X-RAY DIFFRACTION13chain 'B' and (resid 105 through 158 )

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