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- PDB-7me3: YfeA oligomer crystal 3, form 2 -

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Basic information

Entry
Database: PDB / ID: 7me3
TitleYfeA oligomer crystal 3, form 2
ComponentsPeriplasmic chelated iron-binding protein YfeA
KeywordsMETAL TRANSPORT / metal coordination
Function / homology
Function and homology information


cellular response to iron ion / iron ion transport / periplasmic space / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic
Similarity search - Domain/homology
: / : / Iron-binding protein YfeA
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRadka, C.D. / Aller, S.G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Site 2 of the Yersinia pestis substrate-binding protein YfeA is a dynamic surface metal-binding site
Authors: Radka, C.D. / Aller, S.G.
History
DepositionApr 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic chelated iron-binding protein YfeA
B: Periplasmic chelated iron-binding protein YfeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,57010
Polymers72,0982
Non-polymers4738
Water5,386299
1
A: Periplasmic chelated iron-binding protein YfeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2254
Polymers36,0491
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Periplasmic chelated iron-binding protein YfeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3456
Polymers36,0491
Non-polymers2975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.090, 75.850, 106.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Periplasmic chelated iron-binding protein YfeA


Mass: 36048.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: yfeA, YPO2439, y1897, YP_2227 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56952
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.88 Å3/Da / Density % sol: 34.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 32% PEG 4000, 20 mM Bis-Tris propane, pH 6.3, 50 mM sodium chloride, 0.05%(w/v) sodium azide, 10 mM manganese chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.283 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2.25→45.5 Å / Num. obs: 52503 / % possible obs: 99.54 % / Redundancy: 2 % / CC1/2: 0.968 / Net I/σ(I): 7.3
Reflection shellResolution: 2.25→2.33 Å / Mean I/σ(I) obs: 4.32 / Num. unique obs: 5090 / CC1/2: 0.654

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UXS

5uxs


Resolution: 2.25→45.45 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 2513 5.09 %
Rwork0.1663 46891 -
obs0.1689 49404 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.45 Å2 / Biso mean: 22.3236 Å2 / Biso min: 1.89 Å2
Refinement stepCycle: final / Resolution: 2.25→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4354 0 8 299 4661
Biso mean--12.41 25.99 -
Num. residues----554
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.290.2538930.22312578267196
2.29-2.340.24071510.195325742725100
2.34-2.390.24251390.182626032742100
2.39-2.450.23881540.185426362790100
2.45-2.510.24071340.184726022736100
2.51-2.580.23861390.177726452784100
2.58-2.650.25721280.18372600272899
2.65-2.740.25841690.19082590275998
2.74-2.830.28291330.16725942727100
2.83-2.950.20321550.175126082763100
2.95-3.080.23111580.167626112769100
3.08-3.240.22061370.160926242761100
3.24-3.450.20921280.15862606273499
3.45-3.710.20671660.154826202786100
3.71-4.090.22091270.14372621274899
4.09-4.680.19031540.133325952749100
4.68-5.890.18461100.15282641275199
5.89-45.450.1611380.16592543268197
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)
14.3671-0.9065-1.15784.009-0.24383.21460.08360.2339-0.3041-0.36770.09940.40690.4206-0.65850.09920.1272-0.0299-0.04750.0725-0.00640.1065-13.565.671-14.995
21.04260.0965-0.00581.0944-0.00621.34450.0208-0.0122-0.072-0.02130.0312-0.10090.09440.0685-0.03010.04280.0053-0.0110.0505-0.00950.0927-2.1798.937-8.064
32.0207-1.342-0.83243.89032.79664.95010.03160.1284-0.0476-0.3005-0.26350.3195-0.5845-0.14580.01820.10180.0238-0.03610.10780.00920.1106-16.5121.168-16.411
41.3201-0.292-0.25052.13840.20322.27560.0411-0.28640.16890.12850.0819-0.1821-0.11930.086-0.01020.0843-0.0185-0.00560.1066-0.04150.0706-4.51525.08410.376
50.8674-0.1114-0.02212.27030.1692.0837-0.1453-0.2285-0.05530.56120.15680.4608-0.1989-0.0950.1069-0.01320.02080.00660.22310.00050.0704-16.52520.7019.932
62.9457-1.0761-1.11353.4596-0.41411.8053-0.05610.2901-0.237-0.1839-0.00630.38350.3574-0.4414-0.0130.1169-0.0288-0.00810.0653-0.01170.1147-13.38245.332-16.842
70.9995-0.35640.15011.05690.18961.4753-0.04220.0002-0.0299-0.00970.022-0.10790.14980.11020.01710.0514-0.00880.01460.05460.01350.0873-1.93848.492-9.852
81.6437-0.4323-0.3182.63932.77585.85370.1075-0.07130.1386-0.1666-0.13120.0376-0.3428-0.4070.14840.05340.0063-0.01080.1201-0.0010.116-17.71260.471-14.699
91.33790.3827-0.42632.18680.60423.6651-0.1708-0.55360.33350.41410.138-0.2958-0.20160.0964-0.03210.1730.0623-0.03510.208-0.07010.125-4.91959.26712.256
101.4519-0.1785-0.34212.2470.4472.8737-0.1334-0.25270.03560.64940.0480.04850.3823-0.27390.03470.20620.01870.02460.22220.00260.1037-10.85651.49316.688
112.2175-0.1472-0.33761.39840.27082.47260.0803-0.7329-0.16790.5269-0.13360.56050.1313-0.87370.1898-0.1701-0.04010.03660.18910.0260.1117-16.76352.6630.696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 38:67 )A38 - 67
2X-RAY DIFFRACTION2( CHAIN A AND RESID 68:164 )A68 - 164
3X-RAY DIFFRACTION3( CHAIN A AND RESID 165:192 )A165 - 192
4X-RAY DIFFRACTION4( CHAIN A AND RESID 193:248 )A193 - 248
5X-RAY DIFFRACTION5( CHAIN A AND RESID 249:318 )A249 - 318
6X-RAY DIFFRACTION6( CHAIN B AND RESID 38:67 )B38 - 67
7X-RAY DIFFRACTION7( CHAIN B AND RESID 68:164 )B68 - 164
8X-RAY DIFFRACTION8( CHAIN B AND RESID 165:192 )B165 - 192
9X-RAY DIFFRACTION9( CHAIN B AND RESID 193:248 )B193 - 248
10X-RAY DIFFRACTION10( CHAIN B AND RESID 249:279 )B249 - 279
11X-RAY DIFFRACTION11( CHAIN B AND RESID 280:310 )B280 - 310

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