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- PDB-5edf: Crystal structure of the selenomethionine-substituted iron-regula... -

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Basic information

Entry
Database: PDB / ID: 5edf
TitleCrystal structure of the selenomethionine-substituted iron-regulated protein FrpD from Neisseria meningitidis
ComponentsFrpC operon protein
KeywordsUNKNOWN FUNCTION / Selenomethionine-substituted iron-regulated protein FrpD / FrpC-binding protein / novel fold / metal transport
Function / homologyRTX iron-regulated FrpC / RTX iron-regulated protein FrpC / Prokaryotic membrane lipoprotein lipid attachment site profile. / AZIDE ION / RTX iron-regulated protein (frpC)
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 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 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4825
Polymers28,8961
Non-polymers5864
Water4,936274
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-10 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.293, 38.829, 165.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 28896.346 Da / Num. of mol.: 1 / Mutation: 54:MSE; 70:MSE; 156:MSE; 168:MSE
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. ENLYFQG sequence at the C-terminus is a tobacco-etch virus (TEV) protease cleavage site; 3. LE ...Details: Fragment FrpD43-271, where: 1. the sequence position present in the structure is 44-267; 2. ENLYFQG sequence at the C-terminus is a tobacco-etch virus (TEV) protease cleavage site; 3. LE sequence at the C-terminus is a cloning artifact; 4. HHHHHH sequence at the C-terminus is a 6His-tag.
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: LA50_03295 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08840

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Non-polymers , 5 types, 278 molecules

#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 20% (w/v) PEG 8000, 20% (v/v) PEG 400, and 0.1M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionRedundancy: 5.9 % / Number: 100435 / Rmerge(I) obs: 0.057 / Χ2: 3.2 / D res high: 2 Å / D res low: 50 Å / Num. obs: 17108 / % possible obs: 98.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.315010.057.1335.5
3.424.3110.054.4586
2.993.4210.0493.6036.3
2.712.9910.0562.9856.3
2.522.7110.0642.826.3
2.372.5210.0722.4026.3
2.252.3710.0782.1356.2
2.152.2510.0892.0116.3
2.072.1510.1032.0515.1
22.0710.1181.734.3
ReflectionResolution: 1.4→50 Å / Num. obs: 47065 / % possible obs: 94.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.047 / Χ2: 1.073 / Net I/av σ(I): 37.625 / Net I/σ(I): 13 / Num. measured all: 269990
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.454.50.31939630.59380.9
1.45-1.515.60.26544170.58789.8
1.51-1.585.90.19345470.59492.4
1.58-1.665.90.14246280.61993.9
1.66-1.765.80.10147130.64195.2
1.76-1.95.70.07147420.70996.1
1.9-2.095.70.04947980.81896.4
2.09-2.395.60.04349231.09597.7
2.39-3.025.90.05550582.47999.8
3.02-506.70.03452761.93399

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Phasing

PhasingMethod: SAD
Phasing MAD setHighest resolution: 2 Å / Lowest resolution: 50 Å
Phasing MAD set shell
IDResolution (Å)
112.5-50
17.14-12.5
15-7.14
13.85-5
13.12-3.85
12.63-3.12
12.27-2.63
12-2.27
Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

IDB isoFract xFract yFract zOccupancy
131.4666-0.796-0.618-0.2514.388
223.2208-0.701-0.165-0.483.012
327.9486-0.692-0.108-0.3432.097
431.6515-0.847-0.072-0.4722.067
525.8451-0.837-0.096-0.491.21
630.3789-0.644-0.127-0.5031.116
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.5-500.2210.5530853451
7.14-12.50.3560.5860357217140
5-7.140.4160.5720774562212
3.85-50.3930.498013461063283
3.12-3.850.4120.503021521763389
2.63-3.120.4240.498030502597453
2.27-2.630.3780.434041133582531
2-2.270.2550.285051474599548

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.4→25.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.99 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1927 2388 5.1 %RANDOM
Rwork0.1678 ---
obs0.169 44591 94.13 %-
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 max: 196.31 Å2 / Biso mean: 24.593 Å2 / Biso min: 8.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.4→25.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 39 274 2162
Biso mean--34.52 32.99 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221999
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.952713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04724.907108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51915333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.335159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211558
X-RAY DIFFRACTIONr_mcbond_it2.00761156
X-RAY DIFFRACTIONr_mcangle_it3.062101897
X-RAY DIFFRACTIONr_scbond_it3.5416843
X-RAY DIFFRACTIONr_scangle_it5.08712809
LS refinement shellResolution: 1.399→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 137 -
Rwork0.227 2719 -
all-2856 -
obs--78.46 %
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)
14.09640.3240.42883.0650.34954.34720.1005-0.1931-0.11380.2133-0.04450.24510.1475-0.3291-0.0560.0970.03270.0570.1129-0.00060.08-1.86314.2536.822
20.95551.4010.2964.30162.28471.8273-0.0591-0.0016-0.08510.13040.0697-0.00410.23090.0663-0.01070.13120.01190.01070.07730.01510.10785.2795.14132.178
32.22910.9762-0.49230.9766-0.1013.33940.00640.03840.12590.12290.02730.1477-0.1773-0.2867-0.03370.07860.02710.04770.04-0.00310.0701-0.45714.36532.908
40.56790.0471-0.58191.42930.06962.7169-0.0257-0.03270.0819-0.01250.1016-0.0246-0.12750.1717-0.07590.03290.00250.01670.041-0.01660.06079.82516.1125.468
51.9339-1.5566-0.21124.5015-0.48053.77370.0482-0.0370.0617-0.08270.07270.3853-0.4034-0.2674-0.12090.12660.0210.03360.02250.00680.10063.29526.6225.472
60.8850.0596-0.4282.88010.05552.70350.00050.0240.0109-0.2851-0.00690.0312-0.0993-0.09480.00640.03950.00250.01630.0312-0.00050.05295.68614.25319.223
73.9781-0.9483-2.79040.4625-0.18315.0018-0.18960.2252-0.2379-0.08-0.02440.04560.5974-0.25350.21390.2598-0.03790.02390.1804-0.05730.232811.569-1.497.528
83.9767-2.16070.32725.1052-2.37917.7523-0.09550.0441-0.32120.01630.03160.17440.9026-0.01170.06390.12740.00430.00670.1711-0.05610.102316.9822.777-4.151
91.7216-0.05841.01450.6441-0.03752.67940.01390.0455-0.0619-0.01750.01340.00360.05360.1794-0.02730.00790.00750.01170.1682-0.03110.081923.8228.3232.488
101.9379-0.30070.5821.31440.68744.7437-0.040.27640.2372-0.2889-0.01690.0818-0.59340.08890.05690.117-0.0237-0.0030.1640.01120.095615.64517.218-4.69
1112.5256-1.4761-3.99926.1146-5.720122.8221-0.2341-0.0363-0.9317-0.0001-0.0856-0.0851.25350.67530.31970.13280.08110.01350.0796-0.01380.168719.223-0.13213.129
122.5013-1.24290.88825.5741-2.53925.04230.06630.29350.0975-0.39260.0350.2736-0.24970.0011-0.10140.091-0.00690.00710.11380.00960.075212.80116.8473.333
1350.9872-9.8331-18.157278.4974-36.318779.52211.03186.44633.61743.8005-1.48140.5363-7.7302-2.57140.44961.37660.14520.0080.81990.44140.48610.11730.84-1.569
142.34910.3415-0.72712.525-0.09013.6490.04330.0354-0.0053-0.0423-0.0539-0.0468-0.03920.06770.01060.0079-0.00460.01410.0363-0.01140.03110.76111.72913.862
151.5341-0.1892-0.60821.5183-0.82614.01030.0584-0.04560.10450.05470.0353-0.0909-0.25450.4198-0.09370.0251-0.03970.01940.0836-0.02830.055318.49915.80215.212
1617.3835-2.4729-9.151811.1635-0.90378.969-0.2714-0.9631-1.14730.5012-0.15840.10870.68130.74670.42990.15380.045800.1490.0540.147813.533.50929.469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 54
2X-RAY DIFFRACTION2A55 - 71
3X-RAY DIFFRACTION3A72 - 95
4X-RAY DIFFRACTION4A96 - 123
5X-RAY DIFFRACTION5A124 - 136
6X-RAY DIFFRACTION6A137 - 147
7X-RAY DIFFRACTION7A148 - 156
8X-RAY DIFFRACTION8A157 - 162
9X-RAY DIFFRACTION9A163 - 178
10X-RAY DIFFRACTION10A179 - 196
11X-RAY DIFFRACTION11A197 - 202
12X-RAY DIFFRACTION12A203 - 212
13X-RAY DIFFRACTION13A213 - 219
14X-RAY DIFFRACTION14A220 - 240
15X-RAY DIFFRACTION15A241 - 261
16X-RAY DIFFRACTION16A262 - 267

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