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- PDB-4z3j: Crystal structure of the lectin domain of PapG from E. coli BI47 ... -

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Basic information

Entry
Database: PDB / ID: 4z3j
TitleCrystal structure of the lectin domain of PapG from E. coli BI47 in space group P1
ComponentsPapG, lectin domain
KeywordsSUGAR BINDING PROTEIN / UPEC / urinary tract infection / fimbrial adhesin / adhesin / type I pili / PapG / carbohydrate binding
Function / homology
Function and homology information


carbohydrate binding / cell adhesion / metal ion binding
Similarity search - Function
Bacterial adhesin receptor binding domain / PapG, carbohydrate-binding domain / PapG, carbohydrate-binding domain superfamily / PapG carbohydrate binding domain / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PapG, lectin domain / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJakob, R.P. / Navarra, G. / Zihlmann, P. / Stangier, K. / Preston, R.C. / Rabbani, S. / Maier, T. / Ernst, B.
CitationJournal: Chembiochem / Year: 2017
Title: Carbohydrate-Lectin Interactions: An Unexpected Contribution to Affinity.
Authors: Navarra, G. / Zihlmann, P. / Jakob, R.P. / Stangier, K. / Preston, R.C. / Rabbani, S. / Smiesko, M. / Wagner, B. / Maier, T. / Ernst, B.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PapG, lectin domain
B: PapG, lectin domain
C: PapG, lectin domain
D: PapG, lectin domain


Theoretical massNumber of molelcules
Total (without water)91,0234
Polymers91,0234
Non-polymers00
Water3,927218
1
A: PapG, lectin domain


Theoretical massNumber of molelcules
Total (without water)22,7561
Polymers22,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PapG, lectin domain


Theoretical massNumber of molelcules
Total (without water)22,7561
Polymers22,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PapG, lectin domain


Theoretical massNumber of molelcules
Total (without water)22,7561
Polymers22,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PapG, lectin domain


Theoretical massNumber of molelcules
Total (without water)22,7561
Polymers22,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.760, 56.560, 70.940
Angle α, β, γ (deg.)112.76, 102.76, 88.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PapG, lectin domain


Mass: 22755.660 Da / Num. of mol.: 4 / Fragment: residues 20-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: G801_04654, G801_04690 / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): 494 / References: UniProt: T7DCJ2, UniProt: A0A182DW20*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.77 % / Description: thin plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 30 % PEG2000 MME, 0.15 M KBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99986 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 2.5→52.068 Å / Num. obs: 23326 / % possible obs: 95.15 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.5
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.5 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J8S

1j8s


Resolution: 2.5→52.068 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 1167 5 %
Rwork0.2193 --
obs0.2207 23326 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→52.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6395 0 0 218 6613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036607
X-RAY DIFFRACTIONf_angle_d0.8538989
X-RAY DIFFRACTIONf_dihedral_angle_d11.772339
X-RAY DIFFRACTIONf_chiral_restr0.034919
X-RAY DIFFRACTIONf_plane_restr0.0031155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.61390.34891460.29852760X-RAY DIFFRACTION95
2.6139-2.75170.35151450.28312760X-RAY DIFFRACTION94
2.7517-2.92410.27111460.26882767X-RAY DIFFRACTION96
2.9241-3.14980.30461480.24352806X-RAY DIFFRACTION96
3.1498-3.46670.25451440.22712749X-RAY DIFFRACTION95
3.4667-3.96820.23151440.20362743X-RAY DIFFRACTION93
3.9682-4.99890.17481470.16622788X-RAY DIFFRACTION96
4.9989-52.0790.19771470.18272786X-RAY DIFFRACTION96
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)
10.5874-0.4285-0.38120.0447-0.04811.9828-0.1246-0.12430.04220.13090.01520.1176-0.0850.21850.02150.32020.0572-0.0610.1645-0.01610.2029-10.27385.7097-21.8822
20.84150.04520.39910.2595-0.28751.4439-0.0896-0.1409-0.0376-0.05580.10870.00910.0268-0.2495-0.12430.30910.05830.03310.17760.01270.2958-10.50126.8078-14.0966
32.80620.1875-1.25381.17331.83083.74670.1893-0.4434-0.0219-0.3987-0.3346-0.12680.01530.68690.04040.33220.1327-0.02770.16850.05790.20352.37823.1972-34.6686
41.62990.5601-0.2072.1525-1.15722.22740.2243-0.00190.1875-0.0729-0.1341-0.2253-0.49440.6748-0.05590.3980.0896-0.01570.38670.05150.2454-2.436511.8463-14.5793
50.6880.3925-0.56250.1752-0.12821.7723-0.14170.2304-0.1211-0.1322-0.174-0.1610.2225-0.67580.15180.31540.0580.05630.4364-0.01170.3687-18.00426.7705-10.4698
61.9322-0.5677-1.0171.83132.74664.3078-0.05740.16380.1154-0.46580.0977-0.0444-0.95340.5687-0.18190.2563-0.0265-0.02890.12470.03460.15742.33186.7266-39.1271
71.0948-0.1799-1.5883-0.22660.19473.6116-0.0218-0.1822-0.0865-0.03310.00090.02910.06040.21150.02170.31330.0511-0.01970.2102-0.01010.192-5.79924.2378-21.4189
82.80080.2039-1.3020.7661-0.40574.03850.00480.24820.0818-0.13710.08110.08250.0109-0.1676-0.1230.22510.0324-0.04420.1838-0.02830.2689-8.293633.7726-23.3031
92.09970.2236-1.3594-0.56490.31062.2616-0.0812-0.1557-0.0591-0.0389-0.00710.12130.060.2360.06780.30330.02450.01110.15030.04420.2474-5.704534.7063-19.1968
100.44940.322-0.09110.20940.8035.61380.0860.01370.17030.02430.0349-0.1514-0.1369-0.5529-0.18780.22870.0088-0.04180.2965-0.0170.242212.967850.383128.3275
110.678-0.0786-0.60310.55670.49081.48180.09950.07760.11240.1210.0171-0.09860.07360.1473-0.09120.1993-0.0114-0.01660.16980.0190.185817.4149.051112.9735
121.44670.96720.3163.0253-1.5171.59490.2786-0.1629-0.66161.1382-0.40220.07050.2001-1.1076-0.01640.6886-0.16660.0290.7601-0.05920.08983.365647.544437.5766
130.8613-0.7033-0.34640.75180.71191.9667-0.06630.14460.1095-0.0395-0.10750.12330.05190.2620.02430.2136-0.0552-0.00140.1439-0.04720.301814.741652.652115.3029
141.3974-0.49180.0115-0.1670.21343.8731-0.0051-0.102-0.0854-0.0743-0.05540.17050.0719-0.61420.04170.2124-0.07280.00870.19720.01860.17739.730248.446827.6153
152.13680.6401-2.77311.5510.99626.4273-0.1492-0.604-0.20790.4713-0.38190.18560.24991.00210.18320.2749-0.0961-0.04430.28070.03130.294212.133122.450629.6826
161.4850.4291-1.9960.387-1.20144.5613-0.0129-0.0647-0.02990.0844-0.0924-0.1208-0.17060.17260.08930.1877-0.01490.01510.18040.01220.262511.097622.072719.2962
170.44130.0015-0.64950.4133-0.51694.8003-0.1379-0.455-0.43540.1162-0.415-0.41330.7323-0.2777-0.05930.2168-0.0839-0.17580.31670.07230.30147.721316.884631.1333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 111 )
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 133 )
6X-RAY DIFFRACTION6chain 'A' and (resid 134 through 146 )
7X-RAY DIFFRACTION7chain 'A' and (resid 147 through 195 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 44 )
9X-RAY DIFFRACTION9chain 'B' and (resid 45 through 195 )
10X-RAY DIFFRACTION10chain 'C' and (resid 0 through 26 )
11X-RAY DIFFRACTION11chain 'C' and (resid 27 through 67 )
12X-RAY DIFFRACTION12chain 'C' and (resid 68 through 84 )
13X-RAY DIFFRACTION13chain 'C' and (resid 85 through 133 )
14X-RAY DIFFRACTION14chain 'C' and (resid 134 through 195 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 34 )
16X-RAY DIFFRACTION16chain 'D' and (resid 35 through 174 )
17X-RAY DIFFRACTION17chain 'D' and (resid 175 through 195 )

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