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- PDB-4qq1: Crystal structure of the isotype 1 Transferrin binding protein B ... -

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Basic information

Entry
Database: PDB / ID: 4qq1
TitleCrystal structure of the isotype 1 Transferrin binding protein B (TbpB) from serogroup B Neisseria meningitidis
ComponentsTransferrin-binding protein 2
KeywordsPROTEIN BINDING / Vaccine candidate / transferrin receptor / iron acquisition / surface lipoprotein / host-pathogen interaction / Iron piracy / Transferrin binding / outer-membrane
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Lipocalin - #240 / Lipocalin - #250 / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / Transferrin-binding protein B, N-lobe handle / TbpB, N-lobe handle domain superfamily / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B ...Lipocalin - #240 / Lipocalin - #250 / Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / Transferrin-binding protein B, N-lobe handle / TbpB, N-lobe handle domain superfamily / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Transferrin-binding protein B
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.33 Å
AuthorsCalmettes, C. / Moraes, T.F.
CitationJournal: Microbiologyopen / Year: 2015
Title: Patterns of structural and sequence variation within isotype lineages of the Neisseria meningitidis transferrin receptor system.
Authors: Adamiak, P. / Calmettes, C. / Moraes, T.F. / Schryvers, A.B.
History
DepositionJun 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transferrin-binding protein 2
B: Transferrin-binding protein 2
C: Transferrin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,71314
Polymers178,3703
Non-polymers1,34311
Water54030
1
A: Transferrin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0806
Polymers59,4571
Non-polymers6245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transferrin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8154
Polymers59,4571
Non-polymers3583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transferrin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8184
Polymers59,4571
Non-polymers3623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.330, 99.971, 160.157
Angle α, β, γ (deg.)90.000, 93.470, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-603-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA43 - 576
211chain BB42 - 574
311chain CC42 - 575

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Components

#1: Protein Transferrin-binding protein 2 / TBP-2


Mass: 59456.605 Da / Num. of mol.: 3 / Fragment: unp residued 58-599
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: serogroup B, strain B16B6 / Gene: tbpB, tbp2 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06988
#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cs
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 275 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.2M cesium chloride, sodium citrate pH 5.8, 1.8M ammonium sulfate, 15% glycerol, vapor diffusion, hanging drop, temperature 275K

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Data collection

DiffractionMean temperature: 50 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.33→50 Å / Num. obs: 60615 / % possible obs: 98.671 % / Redundancy: 7.4 % / Biso Wilson estimate: 98.71 Å2 / Rmerge(I) obs: 0.1 / Χ2: 1.891 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Χ2Diffraction-IDRmerge(I) obsNum. unique all% possible all
1.2881
1.2671
1.3511
1.391
1.4261
3.33-3.417.51.47110.673201397.5
3.41-3.57.51.51610.495206397.5
3.5-3.597.51.54410.407202498.1
3.59-3.77.51.6510.311206398.1
3.7-3.827.51.73510.261204598
3.82-3.957.51.82110.201203998.4
3.95-4.117.51.90910.169207898.5
4.11-4.37.51.90310.145204498.9
4.3-4.537.51.92610.104208098.9
4.53-4.817.51.97810.086207599
4.81-5.187.52.10710.079209299.2
5.18-5.77.52.08110.082210999.5
5.7-6.527.52.1610.074209899.7
6.52-8.217.42.47610.058211599.8
8.21-507.24.64610.044216999.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.7 Å40.19 Å
Translation2.7 Å40.19 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.33→45.167 Å / SU ML: 0.56 / σ(F): 1.34 / Phase error: 36.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3012 1440 4.94 %
Rwork0.2491 --
obs0.2516 60408 98.5 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 488.15 Å2 / Biso mean: 124.4591 Å2 / Biso min: 30 Å2
Refinement stepCycle: LAST / Resolution: 3.33→45.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11773 0 25 30 11828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412016
X-RAY DIFFRACTIONf_angle_d0.98416123
X-RAY DIFFRACTIONf_chiral_restr0.0741669
X-RAY DIFFRACTIONf_plane_restr0.0042120
X-RAY DIFFRACTIONf_dihedral_angle_d13.3024416
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6836X-RAY DIFFRACTION17.262TORSIONAL
12B6836X-RAY DIFFRACTION17.262TORSIONAL
13C6836X-RAY DIFFRACTION17.262TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.33-3.38460.48691720.41932689286198
3.3846-3.44290.37791190.37992696281597
3.4429-3.50550.35541260.34282789291597
3.5055-3.57290.37211520.31912653280597
3.5729-3.64580.43071570.29672703286098
3.6458-3.7250.3321370.27962670280798
3.725-3.81160.32711370.28862759289698
3.8116-3.90690.36941480.27642680282898
3.9069-4.01250.35081520.27392802295498
4.0125-4.13050.28381250.24712673279898
4.1305-4.26370.32151460.25022738288499
4.2637-4.4160.21411500.21462758290899
4.416-4.59260.27311340.21162716285099
4.5926-4.80140.32061440.20522727287199
4.8014-5.05420.25561370.20842756289399
5.0542-5.37040.25121380.21362784292299
5.3704-5.78430.30861480.235227372885100
5.7843-6.3650.30821480.243427832931100
6.365-7.28270.3021320.263327792911100
7.2827-9.16280.26561440.239427782922100
9.1628-45.17070.26921380.23162754289299

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