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- PDB-3zh5: The structure of Haemophilus influenzae protein E -

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Basic information

Entry
Database: PDB / ID: 3zh5
TitleThe structure of Haemophilus influenzae 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 / MOLECULAR REPLACEMENT / Resolution: 1.801 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 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / atom_site_anisotrop / diffrn_source
Item: _atom_site_anisotrop.id / _diffrn_source.pdbx_synchrotron_site
Revision 2.1Nov 20, 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

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Assembly

Deposited unit
A: PROTEIN E
B: PROTEIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4887
Polymers31,0872
Non-polymers4005
Water2,288127
1
A: PROTEIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6983
Polymers15,5441
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7904
Polymers15,5441
Non-polymers2463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.187, 57.258, 61.374
Angle α, β, γ (deg.)90.00, 96.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9995, 0.0064, 0.0293), (-0.0069, -0.9998, -0.0169), (0.0292, -0.0171, 0.9994)
Vector: 21.9732, 0.381, -0.3057)

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Components

#1: Protein PROTEIN E


Mass: 15543.541 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.28 Å3/Da / Density % sol: 46 % / Description: STRUCTURE WAS SOLVED WITH SE_MET FORM
Crystal growDetails: 100 MM SPG BUFFER PH 6.0, 25% W/V POLYETHYLENE GLYCOL 1500.

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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 17, 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: 1.8→29 Å / Num. obs: 115628 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.34
Reflection shellHighest resolution: 1.8 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.64 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.801→26.93 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1426 5.1 %
Rwork0.2007 --
obs0.2023 28179 99.47 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.935 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7973 Å20 Å2-0.716 Å2
2---14.2482 Å20 Å2
3---19.0455 Å2
Refinement stepCycle: LAST / Resolution: 1.801→26.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 26 127 2311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132236
X-RAY DIFFRACTIONf_angle_d1.4193026
X-RAY DIFFRACTIONf_dihedral_angle_d15.803825
X-RAY DIFFRACTIONf_chiral_restr0.086322
X-RAY DIFFRACTIONf_plane_restr0.008387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8007-1.86510.38911550.35822552X-RAY DIFFRACTION97
1.8651-1.93970.28291520.26892659X-RAY DIFFRACTION99
1.9397-2.0280.24391230.23432678X-RAY DIFFRACTION100
2.028-2.13490.23561370.19892691X-RAY DIFFRACTION100
2.1349-2.26850.24631320.1942694X-RAY DIFFRACTION100
2.2685-2.44360.22431360.19682682X-RAY DIFFRACTION100
2.4436-2.68930.23791340.21032681X-RAY DIFFRACTION100
2.6893-3.0780.22941440.20242695X-RAY DIFFRACTION100
3.078-3.87610.22571570.19292688X-RAY DIFFRACTION100
3.8761-26.93320.20481560.17812733X-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)
17.1201-0.22732.85546.485-0.52892.91470.7387-0.96780.00231.4506-0.39040.48790.43080.1205-0.21190.6368-0.13990.05940.4123-0.00270.55525.5479-21.595814.959
23.6251-2.08372.68147.8743-6.47358.16940.10320.0250.16710.05250.00860.75770.0967-0.068-0.06680.1637-0.0277-0.00770.1823-0.05240.31563.7345-8.45383.947
31.02650.6163-0.06971.1951-0.00480.67920.4485-0.58550.17181.4369-0.0314-0.56370.3160.3861-0.4521.4849-0.1606-0.38990.4325-0.14540.480915.9281-15.241824.7365
44.03230.7578-0.2594.6354-1.51825.23930.1562-0.15860.20230.6472-0.14580.39090.27560.018-0.02560.2515-0.0280.01360.1383-0.03860.20049.8076-9.22927.8014
51.6445-1.89650.76352.3276-1.89297.820.2115-0.76620.42521.2302-0.6026-0.1868-0.43961.19720.1610.6036-0.1537-0.0110.4237-0.11020.292316.2105-5.022815.8783
65.35691.3828-0.40141.66040.53420.79070.02020.5602-1.08320.0067-0.04710.52990.2952-0.08930.0740.2728-0.0086-0.06370.246-0.0430.5748.5641-15.365-3.1757
73.9491-4.1868-1.50449.6312-2.79434.34190.24491.7154-0.886-2.257-0.41770.82981.1117-2.0853-0.03460.8066-0.1262-0.37860.8477-0.1631.0794-1.9381-10.5974-9.0034
82.3824-0.674-3.45163.87482.49845.96530.2876-0.51230.21241.5293-0.16220.0955-0.6236-0.2584-0.22760.7369-0.0390.02030.37060.00510.462516.351222.11214.949
93.2049-2.3206-1.2828.32776.21666.84370.00070.0739-0.1870.03950.1305-0.8393-0.06620.2287-0.13410.1788-0.03540.00550.20350.04150.400720.23985.84121.7442
103.70360.2921-0.03642.73020.08932.70260.1718-0.4906-0.11130.9158-0.06670.0908-0.6407-0.09050.03330.5271-0.02320.09240.22250.04610.192811.167511.625512.9308
114.52861.37681.37442.87131.10638.64530.2147-0.5238-0.52121.0294-0.3198-0.0727-0.1583-0.38350.05310.479-0.050.01510.18630.07840.30339.65518.072413.9928
124.31342.4467-0.14045.5182-1.71191.4769-0.05460.54941.25560.15090.13320.0632-0.4794-0.1563-0.07340.28950.01540.04810.24990.05560.536313.463915.599-3.1098
137.4518-4.2415-3.35461.9948-6.04097.58511.00481.29770.8044-3.1606-1.345-1.1114-1.0976-0.4870.19990.97180.16830.39530.68980.09440.845624.759210.9764-8.6388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 26:45)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 46:73)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 74:89)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 90:117)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 118:129)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 130:150)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 151:158)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 25:48)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 49:64)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 65:102)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 103:129)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 130:150)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 151:156)

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