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- PDB-4u9c: STRUCTURE OF THE LBPB N-LOBE FROM NEISSERIA MENINGITIDIS -

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Basic information

Entry
Database: PDB / ID: 4u9c
TitleSTRUCTURE OF THE LBPB N-LOBE FROM NEISSERIA MENINGITIDIS
ComponentsLactoferrin-binding protein B
KeywordsLactoferrin-binding protein / beta barrel / lipoprotein / lactoferrin / transferrin
Function / homologyLipocalin - #250 / Porin - #90 / Porin / Lipocalin / Beta Barrel / Mainly Beta / :
Function and homology information
Biological speciesNeisseria meningitidis CU385 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsBrooks, C.L. / Arutyunova, E. / Lemieux, M.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: The structure of lactoferrin-binding protein B from Neisseria meningitidis suggests roles in iron acquisition and neutralization of host defences.
Authors: Brooks, C.L. / Arutyunova, E. / Lemieux, M.J.
History
DepositionAug 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_validate_symm_contact / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactoferrin-binding protein B
B: Lactoferrin-binding protein B


Theoretical massNumber of molelcules
Total (without water)77,7282
Polymers77,7282
Non-polymers00
Water6,738374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.870, 65.020, 83.390
Angle α, β, γ (deg.)90.00, 105.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA27 - 330
211chain BB28 - 330
Detailsbiological unit is the same as asym.

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Components

#1: Protein Lactoferrin-binding protein B


Mass: 38863.773 Da / Num. of mol.: 2 / Fragment: UNP residues 20-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis CU385 (bacteria)
Gene: NMBCU385_0651 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: F0AS41
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 9, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.995→57.7 Å / Num. obs: 43471 / % possible obs: 96.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDRejects% possible allMean I/σ(I) obs
1.995-23.50.3591092.1
10.91-62.792.80.0261097.818.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.995→35.095 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 2107 5.05 %
Rwork0.173 --
obs0.175 41761 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 1.995→35.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4722 0 0 374 5096
Biso mean---41.71 -
Num. residues----586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084819
X-RAY DIFFRACTIONf_angle_d1.1116478
X-RAY DIFFRACTIONf_dihedral_angle_d13.4751821
X-RAY DIFFRACTIONf_chiral_restr0.047662
X-RAY DIFFRACTIONf_plane_restr0.005860
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3426X-RAY DIFFRACTION11.154TORSIONAL
12B3426X-RAY DIFFRACTION11.154TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.995-2.04140.2571420.23012468X-RAY DIFFRACTION94
2.0414-2.09250.23891350.21082663X-RAY DIFFRACTION100
2.0925-2.1490.28651370.1912647X-RAY DIFFRACTION100
2.149-2.21220.25721400.18772663X-RAY DIFFRACTION100
2.2122-2.28360.24321360.18922618X-RAY DIFFRACTION100
2.2836-2.36520.23461450.18532630X-RAY DIFFRACTION100
2.3652-2.45990.25661450.18622677X-RAY DIFFRACTION100
2.4599-2.57180.25591350.18162657X-RAY DIFFRACTION100
2.5718-2.70740.26871550.18362646X-RAY DIFFRACTION100
2.7074-2.87690.19591310.17762667X-RAY DIFFRACTION100
2.8769-3.09890.20891240.17132667X-RAY DIFFRACTION100
3.0989-3.41060.21771570.16432651X-RAY DIFFRACTION99
3.4106-3.90350.18781520.15242610X-RAY DIFFRACTION99
3.9035-4.91590.14641370.14552642X-RAY DIFFRACTION98
4.9159-35.10070.21741360.18542748X-RAY DIFFRACTION100
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)
10.50610.42460.25262.0471-0.4012.13520.0806-0.12970.050.3204-0.1130.02970.08020.15310.02060.2287-0.0095-0.00560.271-0.02150.294-6.0656-19.4467-28.6781
20.7872-0.19310.03611.6366-0.83381.24980.0789-0.0575-0.01080.0878-0.1549-0.37920.01490.25030.08080.1902-0.0089-0.02570.2670.00530.2885-0.5-13.2386-36.8129
31.73560.78790.14710.38810.15581.3077-0.05910.0990.269-0.1139-0.0624-0.755-0.21390.7237-0.10680.2605-0.01050.08290.48050.0780.545.8941-6.7192-50.6871
41.00490.1567-0.30062.7395-0.3281.62920.08540.09250.0739-0.0754-0.07630.0067-0.0558-0.03130.02670.19510.0144-0.02710.22820.01520.2987-8.6128-7.8341-44.8531
50.6736-0.3539-0.5753.7951.25161.3060.0682-0.05970.09840.281-0.0678-0.00690.0356-0.2261-0.01640.2842-0.00940.00820.318-0.01250.2048-13.1927-20.00078.0647
61.2487-0.9247-0.32.19971.11472.3386-0.14570.0003-0.1850.3802-0.09680.7130.3663-0.59780.16370.4519-0.13230.0450.5616-0.05310.3453-26.2958-35.17423.4689
70.40150.4974-0.36893.25161.30031.35790.19340.01130.14510.0548-0.38740.2961-0.0023-0.33170.1780.28830.01980.03640.3633-0.03480.2967-21.2578-17.2838.2761
80.2873-0.3005-0.14442.39751.09661.55160.096-0.04060.0308-0.0057-0.12220.0345-0.1009-0.19260.02670.275-0.02770.00880.3187-0.02310.2483-15.0266-30.0476-4.6662
91.11021.41390.27862.78681.93742.56060.0785-0.0878-0.0318-0.2389-0.1440.2464-0.4585-0.60920.14140.27750.03480.00230.3819-0.05480.294-23.3106-25.2587-6.8337
101.37520.57820.98190.33590.34510.7402-0.02380.03270.0992-0.0373-0.06140.13370.1016-0.08180.10430.2666-0.03650.00380.3014-0.00820.2315-17.8392-37.9835-14.6479
111.1995-0.79720.4842.0288-0.80410.54930.02530.154-0.12450.1834-0.1544-0.01260.10760.07850.09890.3245-0.0193-0.030.25080.00440.2374-5.1215-37.1083-7.584
120.3880.0033-0.08441.72810.31551.73820.07370.0254-0.020.1229-0.0984-0.00180.1292-0.13230.04010.2552-0.01920.00170.2864-0.01140.2271-9.3725-32.0103-6.8405
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 41:102 )A41 - 102
2X-RAY DIFFRACTION2( CHAIN A AND RESID 103:229 )A103 - 229
3X-RAY DIFFRACTION3( CHAIN A AND RESID 230:252 )A230 - 252
4X-RAY DIFFRACTION4( CHAIN A AND RESID 253:330 )A253 - 330
5X-RAY DIFFRACTION5( CHAIN B AND RESID 42:93 )B42 - 93
6X-RAY DIFFRACTION6( CHAIN B AND RESID 94:113 )B94 - 113
7X-RAY DIFFRACTION7( CHAIN B AND RESID 114:153 )B114 - 153
8X-RAY DIFFRACTION8( CHAIN B AND RESID 154:198 )B154 - 198
9X-RAY DIFFRACTION9( CHAIN B AND RESID 202:218 )B202 - 218
10X-RAY DIFFRACTION10( CHAIN B AND RESID 219:252 )B219 - 252
11X-RAY DIFFRACTION11( CHAIN B AND RESID 253:274 )B253 - 274
12X-RAY DIFFRACTION12( CHAIN B AND RESID 275:330 )B275 - 330

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