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- PDB-3uaq: Crystal Structure of the N-lobe Domain of Lactoferrin Binding Pro... -

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Basic information

Entry
Database: PDB / ID: 3uaq
TitleCrystal Structure of the N-lobe Domain of Lactoferrin Binding Protein B (LbpB) of Moraxella bovis
ComponentsLbpB B-lobe
KeywordsPROTEIN BINDING / beta barrel / lipoprotein
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Lipocalin - #250 / 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 ...Lipocalin - #250 / 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
Biological speciesMoraxella bovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9318 Å
AuthorsArutyunova, E. / Brooks, C.L. / Beddeck, A. / Mak, M.W. / Schryvers, A.B. / Lemieux, M.J.
CitationJournal: Biochem.Cell Biol. / Year: 2012
Title: Crystal structure of the N-lobe of lactoferrin binding protein B from Moraxella bovis(1).
Authors: Arutyunova, E. / Brooks, C.L. / Beddek, A. / Mak, M.W. / Schryvers, A.B. / Lemieux, M.J.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Structure summary / Category: audit_author / software
Item: _audit_author.name / _software.classification ..._audit_author.name / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LbpB B-lobe
B: LbpB B-lobe


Theoretical massNumber of molelcules
Total (without water)74,9942
Polymers74,9942
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: LbpB B-lobe


Theoretical massNumber of molelcules
Total (without water)37,4971
Polymers37,4971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: LbpB B-lobe


Theoretical massNumber of molelcules
Total (without water)37,4971
Polymers37,4971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.599, 83.928, 98.589
Angle α, β, γ (deg.)90.00, 101.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 54:163 or resseq 169:188 or resseq 200:342 )
211chain B and (resseq 54:163 or resseq 169:188 or resseq 200:342 )

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Components

#1: Protein LbpB B-lobe


Mass: 37497.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella bovis (bacteria) / Gene: LbpB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H9KVH9*PLUS

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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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: PEG 6000, pH 8.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 7, 2010 / Details: mirrors
RadiationMonochromator: Double Crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.9→96.8 Å / Num. obs: 14327 / % possible obs: 98.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.9-3.063.20.351199.6
3.06-3.183.30.308198.9
3.18-3.323.30.237199.5
3.32-3.53.30.191199
3.5-3.723.30.136199
3.72-43.30.109198.8
4-4.43.30.093198.6
4.4-5.043.30.074198.1
5.04-6.343.30.076197.8
6.34-353.30.068196.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HOL

3hol


Resolution: 2.9318→33.033 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.72 / σ(F): 1.36 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2687 721 5.04 %
Rwork0.2202 --
obs0.2226 14308 97.05 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.597 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7953 Å2-0 Å23.9522 Å2
2---0.3348 Å2-0 Å2
3---3.1301 Å2
Refinement stepCycle: LAST / Resolution: 2.9318→33.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 0 0 4326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054423
X-RAY DIFFRACTIONf_angle_d0.9335965
X-RAY DIFFRACTIONf_dihedral_angle_d18.7281614
X-RAY DIFFRACTIONf_chiral_restr0.06613
X-RAY DIFFRACTIONf_plane_restr0.003794
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2152X-RAY DIFFRACTIONPOSITIONAL
12B2152X-RAY DIFFRACTIONPOSITIONAL0.03
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9318-3.1580.33491370.25712548X-RAY DIFFRACTION92
3.158-3.47550.28811450.24372772X-RAY DIFFRACTION99
3.4755-3.97760.25781500.21942750X-RAY DIFFRACTION99
3.9776-5.00860.26011440.18862753X-RAY DIFFRACTION98
5.0086-33.0350.24591450.22522764X-RAY DIFFRACTION97
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)
10.6130.2172-0.00751.42770.96581.5461-0.0035-0.15660.01960.08520.204-0.021-0.04460.02210.06910.1987-0.0423-0.01440.2625-0.00350.069223.4296-18.535624.6913
20.3636-0.11690.0931.70810.23750.498-0.07990.00910.04930.05760.0505-0.11580.03450.0967-0.30510.039-0.0309-0.00120.1538-0.06910.080823.4808-14.296131.072
30.66290.04450.11570.9650.13271.0074-0.0315-0.00650.0644-0.05710.0384-0.1192-0.13970.0452-0.11950.0995-0.01280.05390.0191-0.01590.12919.55822.674222.9989
40.2409-0.00260.07640.47120.12520.3569-0.00990.038-0.1107-0.05040.1451-0.1647-0.03640.09670.09230.09060.02210.04520.0149-0.05830.18215.644-11.910524.9871
51.9324-0.3728-1.12311.60890.51191.03140.02990.33360.0709-0.0065-0.00330.321-0.0286-0.2501-0.04930.0995-0.00270.04740.10520.05960.11386.5288-9.284120.7829
60.2283-0.0436-0.08830.2566-0.01070.1456-0.0421-0.2054-0.04550.18440.11770.08310.00080.03550.2920.1320.07510.19450.33940.03130.09630.376-5.180938.2583
71.3419-0.7416-0.61160.4480.02852.6691-0.0953-0.0862-0.09340.2532-0.22230.15070.2968-0.29510.01570.0989-0.0028-0.02910.12690.08910.16255.3571-15.011838.9245
80.3322-0.0710.27790.2067-0.07580.5365-0.0011-0.1208-0.04990.04980.0052-0.02750.1043-0.0694-0.11230.18280.1067-0.06690.24910.07930.08210.566-5.33739.9978
90.2796-0.10050.13070.73860.08790.7039-0.0206-0.0277-0.0103-0.0661-0.1311-0.0648-0.01160.1988-0.17770.0702-0.0139-0.01190.20020.10340.143721.201719.00047.8104
100.65780.13860.18780.9721-0.10260.8835-0.0304-0.050.14920.1809-0.1553-0.1326-0.05970.047-0.34770.1158-0.0205-0.00020.07480.00690.223417.436937.97939.9904
110.2092-0.0018-0.11310.2860.06570.5021-0.03280.129-0.0918-0.1963-0.0019-0.0953-0.03530.1228-0.16460.0518-0.03860.0366-0.0585-0.1599-0.061713.722324.23196.6173
120.52620.2899-0.09450.402-0.09660.1461-0.04640.11510.0786-0.07160.10310.08560.0156-0.04480.08870.1393-0.09980.05650.09870.00220.1214.360127.86493.5529
130.45340.18030.24160.42110.29910.66340.1524-0.1104-0.04860.10520.03670.0020.21140.03030.13940.1086-0.04410.00040.1169-0.04630.097-1.69824.911921.2923
141.1605-0.4732-0.32590.5499-0.661.8522-0.11780.03230.0271-0.10650.09290.12130.1003-0.0920.15610.17940.03-0.04280.23190.06110.10653.21415.570818.0685
150.5439-0.27520.10910.6125-0.21650.61270.0425-0.02150.03130.08070.09120.1141-0.0823-0.1350.15190.08370.0575-0.10480.01340.05870.10278.498124.046722.7718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 55:72)
2X-RAY DIFFRACTION2chain 'A' and (resseq 73:94)
3X-RAY DIFFRACTION3chain 'A' and (resseq 95:121)
4X-RAY DIFFRACTION4chain 'A' and (resseq 122:213)
5X-RAY DIFFRACTION5chain 'A' and (resseq 214:236)
6X-RAY DIFFRACTION6chain 'A' and (resseq 237:279)
7X-RAY DIFFRACTION7chain 'A' and (resseq 280:299)
8X-RAY DIFFRACTION8chain 'A' and (resseq 300:341)
9X-RAY DIFFRACTION9chain 'B' and (resseq 55:95)
10X-RAY DIFFRACTION10chain 'B' and (resseq 96:121)
11X-RAY DIFFRACTION11chain 'B' and (resseq 122:213)
12X-RAY DIFFRACTION12chain 'B' and (resseq 214:236)
13X-RAY DIFFRACTION13chain 'B' and (resseq 237:279)
14X-RAY DIFFRACTION14chain 'B' and (resseq 280:299)
15X-RAY DIFFRACTION15chain 'B' and (resseq 300:341)

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