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- PDB-2xzr: Escherichia coli Immunoglobulin-binding protein EibD 391-438 FUSE... -

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Basic information

Entry
Database: PDB / ID: 2xzr
TitleEscherichia coli Immunoglobulin-binding protein EibD 391-438 FUSED TO GCN4 ADAPTORS
ComponentsIMMUNOGLOBULIN-BINDING PROTEIN EIBD
KeywordsCELL ADHESION / TRIMERIC AUTOTRANSPORTER ADHESIN / TAA / PROTEIN EXPORT
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
Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Serralysin-like metalloprotease, C-terminal / Pilin-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin-binding protein EibD
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE P-EIBD (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHartmann, M.D. / Hernandez Alvarez, B. / Ridderbusch, O. / Deiss, S. / Lupas, A.N.
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
DepositionNov 28, 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 / pdbx_struct_special_symmetry / 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

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Assembly

Deposited unit
A: IMMUNOGLOBULIN-BINDING PROTEIN EIBD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6945
Polymers13,5531
Non-polymers1424
Water1086
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)41,08315
Polymers40,6583
Non-polymers42512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area12850 Å2
ΔGint-188.9 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.670, 36.670, 228.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1001-

CL

21A-1002-

CL

31A-1003-

CL

41A-1004-

CL

51A-2005-

HOH

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Components

#1: Protein IMMUNOGLOBULIN-BINDING PROTEIN EIBD


Mass: 13552.596 Da / Num. of mol.: 1 / Fragment: RESIDUES 391-438
Source method: isolated from a genetically manipulated source
Details: N- AND C-TERMINAL IN-REGISTER FUSION TO GCN4 ADAPTORS
Source: (gene. exp.) ENTEROBACTERIA PHAGE P-EIBD (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9MCI8
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMKQIEDKIEEILSKIYHIENEIARIKKLI IS AN N-TERMINAL TAG BASED ON THE SEQUENCE OF A GCN4 ADAPTOR DOMAIN. ...MKQIEDKIEEILSKIYHIENEIARIKKLI IS AN N-TERMINAL TAG BASED ON THE SEQUENCE OF A GCN4 ADAPTOR DOMAIN. QIEDKIEEILSKIYHIENEIARIKKLIKL IS A C-TERMINAL TAG BASED ON THE SEQUENCE OF A GCN4 ADAPTOR DOMAIN. THERE IS AN ADDITIONAL ENGINEED HEXAHISTIDINE C-TERMINAL TAG.

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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: 3.5 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 7.5
Details: 20% (V/V) 2-PROPANOL, 200 MM SODIUM CITRATE, 100 MM HEPES PH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→38.1 Å / Num. obs: 4931 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 2.81 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.77
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 2.92 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.09 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WPQ

2wpq


Resolution: 2.8→38.1 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.913 / SU B: 36.008 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R: 0.765 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30775 541 11 %RANDOM
Rwork0.25967 ---
obs0.26509 4374 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.006 Å2
Baniso -1Baniso -2Baniso -3
1-6.51 Å23.26 Å20 Å2
2--6.51 Å20 Å2
3----9.77 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms869 0 4 6 879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022875
X-RAY DIFFRACTIONr_bond_other_d0.0010.02605
X-RAY DIFFRACTIONr_angle_refined_deg1.061.9521172
X-RAY DIFFRACTIONr_angle_other_deg0.79131492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9055107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71425.68244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.19415187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.557156
X-RAY DIFFRACTIONr_chiral_restr0.0510.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02949
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02149
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_it0.7511.5537
X-RAY DIFFRACTIONr_mcbond_other0.0911.5217
X-RAY DIFFRACTIONr_mcangle_it1.4892870
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9693338
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6084.5302
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 37 -
Rwork0.312 304 -
obs--100 %
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)
143.3434-5.63046.833515.9842-13.605358.6296-0.26912.38242.1038-1.26-0.8426-0.4455-1.94411.19711.11180.57320.029-0.01720.41060.06060.391724.666-7.357-7.669
217.9558-14.0465.311.0695-5.928440.3969-0.15010.05750.67910.1627-0.1176-0.5358-0.23592.60330.26770.1947-0.0988-0.04210.3185-0.00420.304424.837-11.55.762
39.4119-9.02314.17219.0245-0.834640.5251-0.55160.3858-0.19250.7368-0.0373-0.00460.78422.97430.58890.2210.0963-0.1090.4131-0.08060.537523.633-14.39219.755
412.187-1.2867-2.08143.6937-12.502245.9213-1.2740.5554-0.7952-0.1201-0.7539-0.47341.20551.86592.02780.6610.04210.07010.6115-0.01690.211421.058-15.89435.413
50.8827-0.3292-6.782615.4305-1.829153.9161-0.27880.0069-0.0593-1.2316-0.36340.48783.2508-0.4390.64210.5112-0.0627-0.04340.6354-0.11020.297416.761-16.36649.183
66.16692.33011.42651.0332-2.152163.9326-0.8979-0.1830.1545-0.3989-0.02870.14951.9274-2.72740.92650.4053-0.0894-0.03140.4161-0.03450.511713.456-14.09965.128
712.172710.171119.031112.648412.809232.06080.2419-1.51780.4554-0.7092-0.99790.17371.2625-2.66910.75610.2878-0.0927-0.01750.5243-0.00180.245312.089-11.44279.322
89.0382-8.1694-1.782110.394314.615156.5517-0.40210.1544-0.0685-0.1085-0.63890.3024-1.7271-1.84171.0410.2836-0.0258-0.10110.3045-0.03330.415412.212-7.38993.89
97.0522-3.82328.91277.18997.539641.2027-0.1949-0.2195-0.3154-0.111-0.27090.5487-0.8984-1.28640.46590.3465-0.02140.00990.20260.0950.360714.1-5.818108.272
105.9379-1.703813.692714.03167.179740.7094-0.4958-0.08610.1451-0.4237-0.47540.7873-1.6506-0.66680.97120.23470.0364-0.01670.13880.0210.428516.923-4.405122.756
1124.08525.82166.970219.35592.761531.72770.123-1.1518-0.00071.1543-0.2037-0.3298-2.0825-0.34610.08080.330.0356-0.02140.2066-0.01790.288819.643-3.651136.513
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A360 - 371
2X-RAY DIFFRACTION2A372 - 381
3X-RAY DIFFRACTION3A382 - 391
4X-RAY DIFFRACTION4A392 - 401
5X-RAY DIFFRACTION5A402 - 411
6X-RAY DIFFRACTION6A412 - 421
7X-RAY DIFFRACTION7A422 - 431
8X-RAY DIFFRACTION8A432 - 441
9X-RAY DIFFRACTION9A442 - 451
10X-RAY DIFFRACTION10A452 - 461
11X-RAY DIFFRACTION11A462 - 471

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