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- PDB-2xqh: Crystal structure of an immunoglobulin-binding fragment of the tr... -

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Basic information

Entry
Database: PDB / ID: 2xqh
TitleCrystal structure of an immunoglobulin-binding fragment of the trimeric autotransporter adhesin EibD
ComponentsIMMUNOGLOBULIN-BINDING PROTEIN EIBD
KeywordsCELL ADHESION / VIRULENCE / BETA-HELIX
Function / homology
Function and homology information


protein secretion by the type V secretion system / cell outer membrane / cell surface / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1970 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1980 / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1970 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1980 / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Serralysin-like metalloprotease, C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin-binding protein EibD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLeo, J.C. / Lyskowski, A. / Hartmann, M. / Schwarz, H. / Linke, D. / Lupas, A.N. / Goldman, A.
CitationJournal: Structure / Year: 2011
Title: The Structure of E. Coli Igg-Binding Protein D Suggests a General Model for Bending and Binding in Trimeric Autotransporter Adhesins.
Authors: Leo, J.C. / Lyskowski, A. / Hattula, K. / Hartmann, M.D. / Schwarz, H. / Butcher, S.J. / Linke, D. / Lupas, A.N. / Goldman, A.
History
DepositionSep 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: IMMUNOGLOBULIN-BINDING PROTEIN EIBD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1735
Polymers29,0311
Non-polymers1424
Water3,117173
1
A: IMMUNOGLOBULIN-BINDING PROTEIN EIBD
hetero molecules

A: IMMUNOGLOBULIN-BINDING PROTEIN EIBD
hetero molecules

A: IMMUNOGLOBULIN-BINDING PROTEIN EIBD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,51815
Polymers87,0923
Non-polymers42512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area22310 Å2
ΔGint-167.6 kcal/mol
Surface area30950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.950, 48.950, 409.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1418-

CL

21A-1419-

CL

31A-1420-

CL

41A-1421-

CL

51A-2118-

HOH

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Components

#1: Protein IMMUNOGLOBULIN-BINDING PROTEIN EIBD / TRIMERIC AUTOTRANSPORTER ADHESIN EIBD


Mass: 29030.799 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN-BINDING DOMAIN, RESIDUES 160-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: ECOR-9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9MCI8
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.64 Å3/Da / Density % sol: 66.23 % / Description: NONE
Crystal growDetails: 1.0 M AMMONIUM PHOSPHATE, 0.1 M SODIUM CITRATE PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.03892
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03892 Å / Relative weight: 1
ReflectionResolution: 1.99→41.51 Å / Num. obs: 24632 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 33.269 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 30.61
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 3 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 5.89 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P9H

1p9h


Resolution: 1.99→41.512 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 18.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1855 1232 5 %
Rwork0.1585 --
obs0.1599 24621 97.84 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.647 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7363 Å20 Å20 Å2
2--3.7363 Å20 Å2
3----7.4726 Å2
Refinement stepCycle: LAST / Resolution: 1.99→41.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 4 173 2039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081874
X-RAY DIFFRACTIONf_angle_d1.0272534
X-RAY DIFFRACTIONf_dihedral_angle_d13.177668
X-RAY DIFFRACTIONf_chiral_restr0.07304
X-RAY DIFFRACTIONf_plane_restr0.003333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9901-2.06980.24111370.22942574X-RAY DIFFRACTION96
2.0698-2.1640.20561400.19432574X-RAY DIFFRACTION97
2.164-2.2780.21071290.16652573X-RAY DIFFRACTION98
2.278-2.42080.17561400.15772625X-RAY DIFFRACTION98
2.4208-2.60760.20541370.15762585X-RAY DIFFRACTION98
2.6076-2.870.17221360.14172620X-RAY DIFFRACTION98
2.87-3.28520.15551400.14412615X-RAY DIFFRACTION98
3.2852-4.13840.17151360.13872618X-RAY DIFFRACTION99
4.1384-41.5210.19681370.16932605X-RAY DIFFRACTION97
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)
10.3311-0.240.05850.87070.16610.88680.00180.0260.0872-0.0833-0.025-0.088-0.14150.11260.01490.1484-0.0190.01140.1569-0.00070.24166.28529153.9923
21.5911-0.3005-0.89230.8320.4660.98350.213-0.31550.10450.42120.010.0891-0.1675-0.1813-0.16740.27060.02160.04130.2707-0.02020.2082-3.52665.4022176.3733
3-0.4884-0.12480.0648-0.3112-0.00270.4328-0.0009-0.09080.12550.43880.0612-0.13111.12780.08540.02040.979-0.0242-0.0380.7931-0.00070.1376-1.1037-5.6976218.2449
43.46441.3811-0.49970.5466-0.20680.11570.7239-0.6971-0.61310.5599-0.59210.27310.80410.2361-0.35190.929-0.3566-0.05420.7341-0.08320.319-5.8355-11.4459258.2325
50.4896-0.0627-0.51990.7316-0.59832.65190.08170.07350.1221-0.0447-0.0529-0.0027-0.2878-0.28660.05640.18150.02020.01480.1912-0.00350.2429-1.40944.0217287.7682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 160:276 AND NOT ELEMENT H)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 277:305 AND NOT ELEMENT H)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 306:349 AND NOT ELEMENT H)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 350:371 AND NOT ELEMENT H)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 372:417 AND NOT ELEMENT H)

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