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- PDB-3zh7: The structure of crystal form II of Haemophilus influenzae protein E -

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Basic information

Entry
Database: PDB / ID: 3zh7
TitleThe structure of crystal form II of Haemophilus influenzae protein E
Components(PROTEIN E) x 2
KeywordsCELL ADHESION
Function / homology
Function and homology information


cell outer membrane / cell surface
Similarity search - Function
Surface-adhesin protein E, Pasteurellaceae / Surface-adhesin protein E-like / Surface-adhesin protein E / Surface-adhesin protein E / Surface-adhesin protein E / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Surface-adhesin protein E
Similarity search - Component
Biological speciesHAEMOPHILUS INFLUENZAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsSingh, B. / Al-Jubair, T. / Riesbeck, K. / Thunnissen, M.M.G.M.
CitationJournal: Infect.Immun. / Year: 2013
Title: The Unique Structure of Haemophilus Influenzae Protein E Reveals Multiple Binding Sites for Host Factors.
Authors: Singh, B. / Al-Jubair, T. / Morgelin, M. / Thunnissen, M.M. / Riesbeck, K.
History
DepositionDec 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references / Other
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _diffrn_source.pdbx_synchrotron_site
Revision 2.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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: PROTEIN E
B: PROTEIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7064
Polymers29,5822
Non-polymers1242
Water84747
1
A: PROTEIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7822
Polymers14,7201
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9242
Polymers14,8621
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.670, 42.490, 56.800
Angle α, β, γ (deg.)90.00, 116.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2825, -0.2293, -0.9315), (-0.1995, -0.9638, 0.1768), (-0.9383, 0.1359, -0.318)
Vector: 14.9717, -23.3283, 26.0555)

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Components

#1: Protein PROTEIN E


Mass: 14719.706 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4F5U7, UniProt: P43961*PLUS
#2: Protein PROTEIN E


Mass: 14861.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4F5U7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.7 %
Description: STRUCTURE WAS SOLVED WITH STRUCTURE FROM OTHER CRYSTAL FORM OF PE.
Crystal growDetails: 100 MM BISTRIS PROPANE PH 6.5, 200 MM NAI AND 20% W/V POLYETHYLENE GLYCOL 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2011 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29 Å / Num. obs: 12867 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 2.49 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.94
Reflection shellHighest resolution: 2.1 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.03 / % possible all: 79.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.102→28.298 Å / SU ML: 0.57 / σ(F): 2.01 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 671 5 %
Rwork0.2007 --
obs0.2035 13338 96.53 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.955 Å2 / ksol: 0.439 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.034 Å20 Å2-8.6236 Å2
2---6.9686 Å20 Å2
3---8.0025 Å2
Refinement stepCycle: LAST / Resolution: 2.102→28.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 8 47 2145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072152
X-RAY DIFFRACTIONf_angle_d1.0292923
X-RAY DIFFRACTIONf_dihedral_angle_d13.474793
X-RAY DIFFRACTIONf_chiral_restr0.057316
X-RAY DIFFRACTIONf_plane_restr0.003375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1018-2.2640.32791250.27262161X-RAY DIFFRACTION84
2.264-2.49180.25781240.23592619X-RAY DIFFRACTION100
2.4918-2.8520.30081380.22422590X-RAY DIFFRACTION100
2.852-3.59210.25441390.18582626X-RAY DIFFRACTION100
3.5921-28.30030.23381450.18072671X-RAY DIFFRACTION99
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)
16.41040.39972.2423.42411.3744.0684-0.1280.32590.5174-0.11430.00950.7633-0.2407-0.58850.11330.3503-0.0348-0.04240.31590.1520.4482-8.0862-2.56.085
28.47370.8619-2.26952.405-0.95972.9266-0.0624-0.1362-0.07840.24360.21940.55660.0446-0.438-0.12140.2595-0.0038-0.01790.26390.06150.3581-10.6743-10.556213.3913
32.1808-2.67052.93747.3301-0.00596.8381-0.09810.3168-0.0061-1.22890.0870.2126-0.0553-0.0907-0.06890.3298-0.0321-0.060.2866-0.02120.2780.7354-8.7562-0.1201
43.436-0.10480.84413.04521.09197.5673-0.1015-0.63130.21860.4424-0.0107-0.10690.20.1806-0.07670.22970.0221-0.06610.26160.00380.37338.0471-17.054731.8447
53.9899-1.1885-1.74044.13921.06943.5261-0.0991-0.9710.35760.54540.06440.2654-0.4062-0.31550.01460.35070.08380.06960.4512-0.10440.3040.1021-6.702335.9192
63.33840.1216-2.27122.7394-0.44366.55210.0317-0.14720.32350.048-0.04450.3156-0.7537-0.2370.00690.28310.0182-0.07270.2568-0.02940.28374.1978-8.680726.2139
78.91522.97230.33291.8230.35647.6046-0.26510.31550.05920.05410.4139-0.02340.33581.0141-0.31970.34150.0282-0.14470.36730.04710.384617.7708-16.602224.4148
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 27:64)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 65:129)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 130:153)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 26:64)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 65:89)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 90:133)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 134:156)

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