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- PDB-3mcy: Crystal structure of FimH lectin domain bound to biphenyl mannosi... -

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Basic information

Entry
Database: PDB / ID: 3mcy
TitleCrystal structure of FimH lectin domain bound to biphenyl mannoside meta-methyl ester.
ComponentsFimH
Keywordscarbohydrate binding protein / lectin / mannoside / immunogobulin fold
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / metal ion binding
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFord, B.A. / Hultgren, S.J.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Structure-based drug design and optimization of mannoside bacterial FimH antagonists.
Authors: Han, Z. / Pinkner, J.S. / Ford, B. / Obermann, R. / Nolan, W. / Wildman, S.A. / Hobbs, D. / Ellenberger, T. / Cusumano, C.K. / Hultgren, S.J. / Janetka, J.W.
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FimH
D: FimH
B: FimH
C: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,09118
Polymers77,9864
Non-polymers2,10414
Water3,261181
1
A: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0555
Polymers19,4971
Non-polymers5584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9273
Polymers19,4971
Non-polymers4302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0555
Polymers19,4971
Non-polymers5584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0555
Polymers19,4971
Non-polymers5584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)198.820, 198.820, 198.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31B
41C
12A
22D
32C
42B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHETHRTHR4AA1 - 1581 - 158
21PHEPHETHRTHR4DB1 - 1581 - 158
31PHEPHETHRTHR4BC1 - 1581 - 158
41PHEPHETHRTHR4CD1 - 1581 - 158
12ZH1ZH1ZH1ZH11AE182
22ZH1ZH1ZH1ZH11DI182
32ZH1ZH1ZH1ZH11CO182
42ZH1ZH1ZH1ZH11BK182

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ADBC

#1: Protein
FimH


Mass: 19496.621 Da / Num. of mol.: 4 / Fragment: FimH lectin domain, UNP residues 22-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: J96 / Gene: fimH / Plasmid: pTRC99a / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q9S497

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Non-polymers , 5 types, 195 molecules

#2: Chemical
ChemComp-ZH1 / methyl 4'-(alpha-D-mannopyranosyloxy)biphenyl-3-carboxylate


Mass: 390.384 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H22O8
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 4.2 Å3/Da / Density % sol: 70.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Co-crystallized FimH/mannoside 8a in 20% ethanol, 100mM imidazole pH 8.0, 200mM MgCl2. Crystals diffract only after incubation in stabilizing solution containing 15% ethanol, 100mM imidazole ...Details: Co-crystallized FimH/mannoside 8a in 20% ethanol, 100mM imidazole pH 8.0, 200mM MgCl2. Crystals diffract only after incubation in stabilizing solution containing 15% ethanol, 100mM imidazole pH 8.0, 200mM MgCl2, 10% PEG200, 5% glycerol and 1mM compound 8a, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 19, 2009
RadiationMonochromator: Rosenbaum-Rock monochromator 1: double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→70.3 Å / Num. all: 30391 / Num. obs: 30391 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 35.3 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 15.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.6.0041refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UWF

1uwf


Resolution: 2.9→59.95 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 24.793 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.509 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24516 1526 5.1 %RANDOM
Rwork0.21904 ---
obs0.22039 28548 99.1 %-
all-30391 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.316 Å2
Refinement stepCycle: LAST / Resolution: 2.9→59.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4758 0 137 181 5076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225017
X-RAY DIFFRACTIONr_bond_other_d0.0020.023126
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9696900
X-RAY DIFFRACTIONr_angle_other_deg0.7033.0027654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.2435628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99324.573199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26815660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5851516
X-RAY DIFFRACTIONr_chiral_restr0.0670.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021012
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_it0.0270.228361
X-RAY DIFFRACTIONr_mcbond_other0.0210.250028
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1930MEDIUM POSITIONAL0.430.5
12D1930MEDIUM POSITIONAL0.720.5
13B1930MEDIUM POSITIONAL0.50.5
14C1930MEDIUM POSITIONAL0.450.5
11A1930MEDIUM THERMAL1.332
12D1930MEDIUM THERMAL1.842
13B1930MEDIUM THERMAL1.332
14C1930MEDIUM THERMAL1.582
21A43TIGHT POSITIONAL0.110.05
22D43TIGHT POSITIONAL0.30.05
23C43TIGHT POSITIONAL0.110.05
24B43TIGHT POSITIONAL0.110.05
21A43TIGHT THERMAL5.930.5
22D43TIGHT THERMAL9.420.5
23C43TIGHT THERMAL4.790.5
24B43TIGHT THERMAL1.80.5
LS refinement shellResolution: 2.9→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 101 -
Rwork0.397 2105 -
obs--99.95 %
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)
12.9487-0.151.90681.03360.13322.047-0.01620.1330.1758-0.0178-0.06790.0153-0.10990.0230.08410.06420.00030.06320.070.02680.0938-31.0150.742418.9251
23.18561.31250.44862.12920.19950.89670.07130.1945-0.1458-0.15680.04050.06880.0092-0.1604-0.11180.04980.0499-0.05050.2551-0.03930.1192-24.686125.8125.4805
31.1071-0.3320.49763.2632-2.16081.840.0223-0.0671-0.3477-0.09410.15120.40210.3401-0.2074-0.17340.2942-0.08530.02850.15870.03440.3766-55.574623.657624.9775
41.92110.4568-1.98670.5357-0.92222.57240.0880.5214-0.0255-0.18750.08590.24520.2081-0.6044-0.17390.458-0.1825-0.29590.7258-0.11960.5072-31.0101-0.8508-18.638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 158
2X-RAY DIFFRACTION2B1 - 158
3X-RAY DIFFRACTION3C1 - 158
4X-RAY DIFFRACTION4D1 - 158

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