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- PDB-3zh6: The structure of Haemophilus influenzae Se_Met form of protein E -

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Basic information

Entry
Database: PDB / ID: 3zh6
TitleThe structure of Haemophilus influenzae Se_Met form of protein E
ComponentsPROTEIN E
KeywordsCELL ADHESION
Function / homologySurface-adhesin protein E / Lipocalin / Beta Barrel / Mainly Beta / :
Function and homology information
Biological speciesHAEMOPHILUS INFLUENZAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.292 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 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2May 15, 2013Group: Other
Revision 1.3Apr 29, 2015Group: Data collection
Revision 1.4Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 16, 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_conn
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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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


Theoretical massNumber of molelcules
Total (without water)31,0382
Polymers31,0382
Non-polymers00
Water2,144119
1
A: PROTEIN E


Theoretical massNumber of molelcules
Total (without water)15,5191
Polymers15,5191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN E


Theoretical massNumber of molelcules
Total (without water)15,5191
Polymers15,5191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.085, 56.884, 61.315
Angle α, β, γ (deg.)90.00, 97.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9995, -0.0088, 0.0295), (0.009, -0.9999, 0.0069), (0.0294, 0.0072, 0.9995)
Vector: 49.5817, 74.1364, -0.9634)

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Components

#1: Protein PROTEIN E


Mass: 15519.126 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Plasmid: PET26PEL43, 74M / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): 834 / References: UniProt: C4F5U7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.26 Å3/Da / Density % sol: 45.7 % / Description: NONE
Crystal growDetails: 100 MM MES, PH 6, 200 MM NACL AND 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9700, 0.97918, 0.97942
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 7, 2011 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
20.979181
30.979421
ReflectionResolution: 2.3→29 Å / Num. obs: 101090 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.83 % / Biso Wilson estimate: 26.55 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.4
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.85 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
SHELXSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.292→28.93 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 29.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2549 616 4.9 %
Rwork0.1868 --
obs0.1901 12573 92.04 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.062 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.1445 Å20 Å2-9.929 Å2
2---14.7835 Å20 Å2
3---20.928 Å2
Refinement stepCycle: LAST / Resolution: 2.292→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 0 119 2261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092200
X-RAY DIFFRACTIONf_angle_d1.2082985
X-RAY DIFFRACTIONf_dihedral_angle_d13.9817
X-RAY DIFFRACTIONf_chiral_restr0.083316
X-RAY DIFFRACTIONf_plane_restr0.006385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2921-2.52270.34751370.27392673X-RAY DIFFRACTION83
2.5227-2.88740.29761510.23642902X-RAY DIFFRACTION90
2.8874-3.63670.26741710.17923120X-RAY DIFFRACTION96
3.6367-28.93190.20231570.15473262X-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)
10.3194-0.15930.30740.5105-0.23410.51610.24830.11630.0535-0.2775-0.13380.28030.78080.0388-0.05390.47090.0371-0.00850.22260.03170.289629.310315.364547.1118
20.48310.0007-0.0340.875-0.00820.19770.0911-0.11190.2373-0.6624-0.10240.33610.0517-0.06870.52040.28210.0174-0.10470.09170.00440.119926.998927.742252.1354
30.1084-0.0276-0.0055-0.001-0.02650.01410.0546-0.0797-0.1341-0.2696-0.16320.14810.04650.096-0.65740.22580.0242-0.06160.12090.08790.186223.316726.211451.1774
40.4213-0.3982-0.14440.35510.16920.80110.0703-0.0597-0.1342-0.2469-0.01170.1655-0.2114-0.1119-0.00060.18510.0208-0.05380.1019-0.06970.288818.802654.658650.2579
50.60680.06690.03510.70690.1670.42810.0083-0.0982-0.1933-0.316-0.06450.1528-0.0553-0.0095-0.0680.15720.02590.03070.082100.171625.453747.286551.3203
60.09660.06180.07530.13590.10110.1711-0.0114-0.12820.0956-0.3092-0.09250.1892-0.17520.0336-0.36730.28180.1239-0.08720.1149-0.2623-0.030527.781948.082450.2272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 12:49)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 50:107)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 108:142)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 12:59)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 60:108)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 109:140)

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