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- PDB-3ve1: The 2.9 angstrom crystal structure of Transferrin binding protein... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3ve1
TitleThe 2.9 angstrom crystal structure of Transferrin binding protein B (TbpB) from serogroup B M982 Neisseria meningitidis in complex with human transferrin
Components
  • Serotransferrin
  • Transferrin-binding protein 2
KeywordsTRANSPORT PROTEIN / Transferrin receptor / iron acquisition / vaccine candidate / protein-protein complex / host pathogen interaction / Receptor / transferrin / Lipoprotein / Outermembrane protein
Function / homology
Function and homology information


iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade ...iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / basal plasma membrane / cellular response to iron ion / actin filament organization / cell outer membrane / Iron uptake and transport / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / regulation of protein stability / ferrous iron binding / regulation of iron ion transport / HFE-transferrin receptor complex / recycling endosome / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / Clathrin-mediated endocytosis / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / early endosome / blood microparticle / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / plasma 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 / Serotransferrin, mammalian / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Lipocalin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / : / Serotransferrin / Transferrin-binding protein B
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.956 Å
AuthorsCalmettes, C. / Moraes, T.F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: The structural basis of transferrin sequestration by transferrin-binding protein B.
Authors: Calmettes, C. / Alcantara, J. / Yu, R.H. / Schryvers, A.B. / Moraes, T.F.
History
DepositionJan 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Sep 18, 2013Group: Derived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)294,81521
Polymers293,3864
Non-polymers1,42917
Water3,657203
1
A: Transferrin-binding protein 2
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,54612
Polymers146,6932
Non-polymers85310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Transferrin-binding protein 2
D: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,2699
Polymers146,6932
Non-polymers5767
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.023, 153.509, 169.511
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12A
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain B and (resseq 3:212 or resseq 219:333 or resseq...B3 - 212
121chain B and (resseq 3:212 or resseq 219:333 or resseq...B219 - 333
131chain B and (resseq 3:212 or resseq 219:333 or resseq...B337 - 348
141chain B and (resseq 3:212 or resseq 219:333 or resseq...B350 - 679
211chain D and (resseq 3:212 or resseq 219:333 or resseq...D3 - 212
221chain D and (resseq 3:212 or resseq 219:333 or resseq...D219 - 333
231chain D and (resseq 3:212 or resseq 219:333 or resseq...D337 - 348
241chain D and (resseq 3:212 or resseq 219:333 or resseq...D350 - 679
112chain A and (resseq 39:109 or resseq 121:267 or resseq...A39 - 109
122chain A and (resseq 39:109 or resseq 121:267 or resseq...A121 - 267
132chain A and (resseq 39:109 or resseq 121:267 or resseq...A271 - 297
142chain A and (resseq 39:109 or resseq 121:267 or resseq...A303 - 350
152chain A and (resseq 39:109 or resseq 121:267 or resseq...A376 - 417
162chain A and (resseq 39:109 or resseq 121:267 or resseq...A436 - 446
172chain A and (resseq 39:109 or resseq 121:267 or resseq...A476 - 499
182chain A and (resseq 39:109 or resseq 121:267 or resseq...A520 - 620
192chain A and (resseq 39:109 or resseq 121:267 or resseq...A629 - 658
1102chain A and (resseq 39:109 or resseq 121:267 or resseq...A675 - 689
212chain C and (resseq 39:109 or resseq 121:267 or resseq...C39 - 109
222chain C and (resseq 39:109 or resseq 121:267 or resseq...C121 - 267
232chain C and (resseq 39:109 or resseq 121:267 or resseq...C271 - 297
242chain C and (resseq 39:109 or resseq 121:267 or resseq...C303 - 350
252chain C and (resseq 39:109 or resseq 121:267 or resseq...C376 - 417
262chain C and (resseq 39:109 or resseq 121:267 or resseq...C436 - 446
272chain C and (resseq 39:109 or resseq 121:267 or resseq...C476 - 499
282chain C and (resseq 39:109 or resseq 121:267 or resseq...C520 - 620
292chain C and (resseq 39:109 or resseq 121:267 or resseq...C629 - 658
2102chain C and (resseq 39:109 or resseq 121:267 or resseq...C675 - 689

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.999582, -0.015095, -0.024649), (0.013577, -0.998068, 0.060633), (-0.025517, 0.060273, 0.997856)61.490299, -78.006401, 2.23577
2given(-0.997995, -0.023213, -0.058881), (0.019266, -0.997584, 0.06674), (-0.060288, 0.065472, 0.996032)59.4758, -77.953003, 5.15397

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 71406.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: M982 / Gene: tbpB, tbp2 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q09057
#2: Protein Serotransferrin / Transferrin / Beta-1 metal-binding globulin / Siderophilin


Mass: 75286.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TF, PRO1400 / Production host: Pichia pastoris (fungus) / References: UniProt: P02787

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Non-polymers , 4 types, 220 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHOR STATES THAT THE THE DIFFERENCES WITH UNP REFERENCE ARE NATURAL VARIANTS

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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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate pH 6.5, 14% PEG 3350, 0.1M sodium malonate, and 20% glycerol, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 70285 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.115 / Χ2: 1.733 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.95-3.0610.70.6469281.0021100
3.06-3.1810.70.45269591.0631100
3.18-3.3210.70.31369491.1291100
3.32-3.510.70.22269462.2151100
3.5-3.7210.70.15469831.4441100
3.72-410.70.11569951.6291100
4-4.4110.60.08670051.8671100
4.41-5.0410.40.07570382.3921100
5.04-6.3510.20.07871212.4941100
6.35-409.80.04973612.146199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.92 Å39.61 Å
Translation2.92 Å39.61 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.956→37.928 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8072 / SU ML: 0.86 / σ(F): 1.33 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 2497 3.56 %
Rwork0.2072 --
obs0.2087 70132 99.52 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.62 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 228.95 Å2 / Biso mean: 68.9381 Å2 / Biso min: 11.52 Å2
Baniso -1Baniso -2Baniso -3
1-4.3853 Å2-0 Å2-0 Å2
2---2.0857 Å20 Å2
3----2.2996 Å2
Refinement stepCycle: LAST / Resolution: 2.956→37.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18938 0 88 203 19229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119511
X-RAY DIFFRACTIONf_angle_d1.40926242
X-RAY DIFFRACTIONf_chiral_restr0.1052754
X-RAY DIFFRACTIONf_plane_restr0.0063444
X-RAY DIFFRACTIONf_dihedral_angle_d16.6437201
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B5166X-RAY DIFFRACTIONPOSITIONAL0.091
12D5166X-RAY DIFFRACTIONPOSITIONAL0.091
21A4041X-RAY DIFFRACTIONPOSITIONAL0.062
22C4041X-RAY DIFFRACTIONPOSITIONAL0.062
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9559-3.01280.4041270.3173482360993
3.0128-3.07420.3591380.29837263864100
3.0742-3.14110.3621380.281337163854100
3.1411-3.21410.31061380.271237353873100
3.2141-3.29440.29481360.25337103846100
3.2944-3.38340.28891390.236837533892100
3.3834-3.48290.29561380.227837403878100
3.4829-3.59530.26791380.219237513889100
3.5953-3.72370.25131380.217437393877100
3.7237-3.87260.28351400.209737613901100
3.8726-4.04870.25421380.193637483886100
4.0487-4.26190.20491400.17737893929100
4.2619-4.52850.2071390.166537653904100
4.5285-4.87750.17741390.156237853924100
4.8775-5.36710.20811410.182737933934100
5.3671-6.14090.28271410.211138333974100
6.1409-7.72610.23381430.201838533996100
7.7261-37.93140.20291460.19163956410298
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)
14.85452.6804-1.47622.1108-0.99481.47580.0469-0.3677-0.18120.1597-0.0958-0.33190.00840.08030.01160.42330.1102-0.05630.4052-0.21420.468853.5754-66.6188-23.9779
25.64722.4644-3.94077.8483-3.38323.1583-0.95531.16641.67130.2901-1.7154-1.4285-1.09293.17142.43490.6452-0.1606-0.06971.2833-0.00671.337541.9697-50.9752-31.4567
31.63690.8311-0.53171.7509-0.60931.5802-0.10.22920.0222-0.060.1128-0.15010.0809-0.1488-0.01790.35860.09780.02530.3867-0.16870.3145.9703-67.6817-34.8124
40.43921.4151-1.86285.4567-7.22039.5523-0.11111.3958-0.0077-1.7599-1.07611.23911.19020.61090.82521.32860.0431-0.27581.1596-0.21930.88843.7142-59.2172-55.8959
52.03280.1371-1.0182.43020.3053.4676-0.230.4825-0.3784-0.12190.1838-0.47510.41760.05130.0310.4509-0.02690.00090.4366-0.2090.406643.6636-78.0253-37.043
65.95651.76021.74995.4355-0.05936.62120.5761-0.7079-0.30271.184-0.4537-0.997-0.04660.1825-0.17670.5929-0.1849-0.13350.5023-0.00890.494836.1919-87.4978-9.3856
73.02860.37290.81952.29250.54292.37660.4532-0.8346-0.9441.4866-0.40620.19760.6902-0.3452-0.05181.0882-0.5192-0.04470.6595-0.02010.532122.6039-99.6462-3.9552
86.15561.26190.79512.7287-2.14762.25850.5832-0.2365-1.16030.0792-0.7140.7232-0.31590.46070.02670.7454-0.2308-0.08770.4989-0.10770.428126.7375-102.8137-7.3976
94.8963-1.0559-0.10674.9350.10853.99450.05720.22170.1119-0.01260.0599-0.11810.09190.2266-0.09790.23240.0909-0.01290.1951-0.0390.177410.4449-60.7556-11.6105
104.64150.9323-0.17463.3493-0.73994.74270.20760.48840.0434-0.1341-0.00230.69410.3301-0.5867-0.18340.24890.0559-0.04910.39470.07080.3802-21.6934-62.7024-16.7513
115.9772-1.6760.29233.5077-0.31582.72530.47860.6580.1954-0.1421-0.3159-0.05030.21180.0985-0.13060.3224-0.00140.01990.32770.01310.12843.4503-60.2535-17.7843
122.55170.1512-0.2973.27230.0491.9412-0.19270.30850.1823-0.5890.32470.1528-0.00280.1371-0.07750.3474-0.0721-0.16450.3980.20480.3461.6538-38.8826-48.3751
133.23050.0658-0.31831.60750.14823.7141-0.0430.29240.32-0.87650.09320.6537-0.10680.0129-0.0310.3493-0.1222-0.25720.43660.18220.5341-7.9928-41.2148-44.4253
142.5854-0.35730.96990.9778-0.12281.29990.0705-0.30510.71090.1226-0.09860.97520.0467-0.1121-0.03260.21270.0341-0.03440.40350.24210.87749.103-12.2241-26.2962
152.6651.2979-2.29224.2363.02176.7151-0.7532-0.1825-1.97650.26560.27620.07561.03480.52560.50480.63990.07730.59411.4273-0.21561.626520.9978-28.5663-30.8711
160.92560.66020.21942.52080.84571.3887-0.29460.18990.1795-0.21520.23410.5550.04040.03230.06950.3480.0453-0.07970.41960.23840.590617.2457-11.9383-36.8149
176.88130.6189-2.12918.6463-3.69249.60640.2051.2358-0.2488-1.5118-1.3425-0.0547-0.02780.60540.98940.8747-0.2771-0.13931.05510.08880.762420.0794-22.4654-58.4446
181.5470.97580.63362.79430.79242.6457-0.02540.23370.4939-0.23770.11340.7056-0.3266-0.0374-0.1320.2964-0.0107-0.01780.30440.22380.671622.78461.9639-29.2666
193.28251.07040.41473.5411-0.99164.12330.0979-0.48110.30840.9883-0.4620.5626-0.4779-0.23180.30860.7307-0.13430.30830.3943-0.04510.741430.845117.8012-8.3977
208.51671.56745.20817.80672.30323.442-0.1261-1.20630.82382.1246-0.6070.42490.56660.66120.77350.9022-0.27880.11260.5710.05670.558943.878821.2616-4.6725
215.39260.3911.28894.34012.2413.81460.2014-0.92510.16741.24250.1430.26980.1862-0.0771-0.27980.7397-0.17310.18190.50090.07610.617239.024118.1013-5.9417
226.2172-1.4867-0.85794.8903-0.64543.87780.14470.1212-0.3327-0.03710.0370.44850.0855-0.0944-0.19750.33280.0891-0.06150.1548-0.0210.234951.4388-17.3645-11.275
234.7752-0.230.20732.89160.95743.43530.620.79130.2121-0.2901-0.574-0.6016-0.22930.5568-0.05510.32650.20910.08730.38560.06210.222983.9428-15.0978-16.251
244.7262-0.57-0.36712.66080.40982.49560.53920.5056-0.1737-0.2183-0.40210.10270.0839-0.1983-0.10420.32150.0582-0.030.3392-0.02780.117759.9695-18.9534-17.6259
253.50080.05720.42383.4555-0.27682.845-0.21650.4340.02-0.39720.30070.0188-0.0926-0.1708-0.08670.42410.05480.05920.4018-0.13290.285762.1381-41.4558-46.5785
262.66550.30560.33424.23411.03094.1135-0.11880.5823-0.0484-0.63490.0039-0.4899-0.2526-0.25210.06920.4346-0.0130.02520.3654-0.14840.252869.5284-36.8825-42.8683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain C and resid 38:106)C38 - 106
2X-RAY DIFFRACTION2(chain C and resid 107:121)C107 - 121
3X-RAY DIFFRACTION3(chain C and resid 122:262)C122 - 262
4X-RAY DIFFRACTION4(chain C and resid 263:272)C263 - 272
5X-RAY DIFFRACTION5(chain C and resid 273:349)C273 - 349
6X-RAY DIFFRACTION6(chain C and resid 350:534)C350 - 534
7X-RAY DIFFRACTION7(chain C and resid 535:658)C535 - 658
8X-RAY DIFFRACTION8(chain C and resid 675:691)C675 - 691
9X-RAY DIFFRACTION9(chain B and resid 3:92)B3 - 92
10X-RAY DIFFRACTION10(chain B and resid 93:248)B93 - 248
11X-RAY DIFFRACTION11(chain B and resid 249:338)B249 - 338
12X-RAY DIFFRACTION12(chain B and resid 339:601)B339 - 601
13X-RAY DIFFRACTION13(chain B and resid 602:678)B602 - 678
14X-RAY DIFFRACTION14(chain A and resid 38:107)A38 - 107
15X-RAY DIFFRACTION15(chain A and resid 108:121)A108 - 121
16X-RAY DIFFRACTION16(chain A and resid 122:263)A122 - 263
17X-RAY DIFFRACTION17(chain A and resid 264:271)A264 - 271
18X-RAY DIFFRACTION18(chain A and resid 272:440)A272 - 440
19X-RAY DIFFRACTION19(chain A and resid 441:590)A441 - 590
20X-RAY DIFFRACTION20(chain A and resid 591:619)A591 - 619
21X-RAY DIFFRACTION21(chain A and resid 620:689)A620 - 689
22X-RAY DIFFRACTION22(chain D and resid 3:91)D3 - 91
23X-RAY DIFFRACTION23(chain D and resid 92:245)D92 - 245
24X-RAY DIFFRACTION24(chain D and resid 246:340)D246 - 340
25X-RAY DIFFRACTION25(chain D and resid 341:609)D341 - 609
26X-RAY DIFFRACTION26(chain D and resid 610:679)D610 - 679

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