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- PDB-5edj: Crystal structure of the Neisseria meningitidis iron-regulated ou... -

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Basic information

Entry
Database: PDB / ID: 5edj
TitleCrystal structure of the Neisseria meningitidis iron-regulated outer membrane lipoprotein FrpD
ComponentsFrpC operon protein
KeywordsUNKNOWN FUNCTION / Iron-regulated protein FrpD / FrpC-binding protein / novel fold / membrane protein
Function / homologyRTX iron-regulated FrpC / RTX iron-regulated protein FrpC / Prokaryotic membrane lipoprotein lipid attachment site profile. / RTX iron-regulated protein (frpC) / FrpC operon protein
Function and homology information
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSviridova, E. / Bumba, L. / Rezacova, P. / Sebo, P. / Kuta Smatanova, I.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant AgencyP207/11/0717 Czech Republic
Citation
Journal: Sci Rep / Year: 2017
Title: Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis.
Authors: Sviridova, E. / Rezacova, P. / Bondar, A. / Veverka, V. / Novak, P. / Schenk, G. / Svergun, D.I. / Kuta Smatanova, I. / Bumba, L.
#1: Journal: Acta Crystallographica Section F / Year: 2010
Title: Crystallization and preliminary crystallographic characterization of the iron-regulated outer membrane lipoprotein FrpD from Neisseria meningitidis
Authors: Sviridova, E. / Bumba, L. / Rezacova, P. / Prochazkova, K. / Kavan, D. / Bezoushka, K. / Kuty, M. / Sebo, P. / Kuta Smatanova, I.
History
DepositionOct 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.2Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: FrpC operon protein


Theoretical massNumber of molelcules
Total (without water)27,0281
Polymers27,0281
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.390, 115.390, 38.812
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein FrpC operon protein / RTX iron-regulated protein (frpC) / Iron-regulated protein FrpD


Mass: 27027.986 Da / Num. of mol.: 1 / Fragment: UNP residues 43-271
Source method: isolated from a genetically manipulated source
Details: Fragment FrpD43-271, where: 1. the sequence position present in the structure is 44-267; 2. LE sequence at the C-terminus is a cloning artifact
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Gene: LA50_03295 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08840, UniProt: Q9K129*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 13418 / Num. obs: 13324 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 22.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.9 % / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
SCALEPACKdata scaling
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EDF

5edf


Resolution: 2.3→30.65 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 15.477 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24931 668 5 %RANDOM
Rwork0.18287 ---
obs0.18619 12627 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.071 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.07 Å20 Å2
2---0.13 Å20 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 2.3→30.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 0 130 1979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221899
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9342579
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5535223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26725106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51215314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.814158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211497
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.83361118
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.28101822
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6056781
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.35812757
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 39 -
Rwork0.241 855 -
obs--94.2 %
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)
12.11160.70050.43853.49030.84162.61870.0241-0.06370.14570.1312-0.023-0.1687-0.06930.0707-0.00110.190.02840.00850.15720.03570.1491-25.62642.0271.616
21.54260.2248-1.26194.0091.04033.3353-0.0315-0.046-0.05990.343-0.09770.19660.0865-0.19190.12920.2375-0.00140.00490.17240.0380.1196-29.70829.953.121
33.24550.8327-1.87497.11691.01236.0037-0.1834-0.165-0.2355-0.58890.3065-0.28690.20140.4422-0.12310.223-0.0902-0.00660.1874-0.02670.1329-31.5276.201-13.464
42.9645-0.3560.91844.2939-0.90346.95850.18350.0513-0.1076-0.0721-0.16930.21430.58560.2266-0.01420.2302-0.05980.02710.13320.02070.1557-30.8875.513-5.594
50.5747-1.77741.654810.3074-10.413110.796-0.1534-0.0126-0.00270.2636-0.2966-0.3869-0.09370.11560.450.399-0.10990.0210.26030.03650.2258-28.2918.1243.862
61.41331.73880.83986.26210.18391.0971-0.00750.12870.06050.20580.0230.3951-0.0264-0.178-0.01560.2237-0.02760.0510.21050.00790.1279-32.74622.734-3.684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 94
2X-RAY DIFFRACTION2A95 - 153
3X-RAY DIFFRACTION3A154 - 173
4X-RAY DIFFRACTION4A174 - 200
5X-RAY DIFFRACTION5A201 - 220
6X-RAY DIFFRACTION6A221 - 267

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