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- PDB-7uq0: Putative periplasmic iron siderophore binding protein FecB (Rv304... -

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Basic information

Entry
Database: PDB / ID: 7uq0
TitlePutative periplasmic iron siderophore binding protein FecB (Rv3044) from Mycobacterium tuberculosis
ComponentsProbable FEIII-dicitrate-binding periplasmic lipoprotein FecB
Keywordssiderophore binding protein / Periplasm / siderophore
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space / extracellular region / plasma membrane
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
CITRIC ACID / Probable FEIII-dicitrate-binding periplasmic lipoprotein FecB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChao, A. / Cuthbert, B.J. / Goulding, C.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1321846 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095208 United States
CitationJournal: Plos Pathog. / Year: 2023
Title: Differentiating the roles of Mycobacterium tuberculosis substrate binding proteins, FecB and FecB2, in iron uptake.
Authors: de Miranda, R. / Cuthbert, B.J. / Klevorn, T. / Chao, A. / Mendoza, J. / Arbing, M. / Sieminski, P.J. / Papavinasasundaram, K. / Abdul-Hafiz, S. / Chan, S. / Sassetti, C.M. / Ehrt, S. / Goulding, C.W.
History
DepositionApr 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable FEIII-dicitrate-binding periplasmic lipoprotein FecB
B: Probable FEIII-dicitrate-binding periplasmic lipoprotein FecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,98715
Polymers73,0942
Non-polymers1,89413
Water7,458414
1
A: Probable FEIII-dicitrate-binding periplasmic lipoprotein FecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7789
Polymers36,5471
Non-polymers1,2318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable FEIII-dicitrate-binding periplasmic lipoprotein FecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2096
Polymers36,5471
Non-polymers6635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.650, 87.070, 71.730
Angle α, β, γ (deg.)90.000, 104.150, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable FEIII-dicitrate-binding periplasmic lipoprotein FecB


Mass: 36546.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: fecB, Rv3044 / Production host: Escherichia coli (E. coli) / References: UniProt: O53291

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Non-polymers , 5 types, 427 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H8O7
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.1 M Phosphate-citrate pH 3.8, 26% PEG 8000, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→43.54 Å / Num. obs: 105296 / % possible obs: 97.16 % / Redundancy: 2 % / Biso Wilson estimate: 26.78 Å2 / CC1/2: 0.539 / Rmerge(I) obs: 0.0845 / Net I/σ(I): 6.28
Reflection shellResolution: 2→2.072 Å / Redundancy: 2 % / Rmerge(I) obs: 1.039 / Num. unique obs: 5381 / CC1/2: 0.0082 / % possible all: 93.76

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
BOSdata collection
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TNY

3tny


Resolution: 2→43.54 Å / SU ML: 0.2485 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.694
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2222 10543 10.01 %
Rwork0.1889 94753 -
obs0.1922 105296 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.63 Å2
Refinement stepCycle: LAST / Resolution: 2→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4440 0 120 414 4974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434691
X-RAY DIFFRACTIONf_angle_d0.62866411
X-RAY DIFFRACTIONf_chiral_restr0.0437740
X-RAY DIFFRACTIONf_plane_restr0.0044854
X-RAY DIFFRACTIONf_dihedral_angle_d19.2044718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.38243190.34912909X-RAY DIFFRACTION87.88
2.02-2.050.36883350.3333002X-RAY DIFFRACTION90.78
2.05-2.070.33883310.31512970X-RAY DIFFRACTION91.26
2.07-2.10.30773360.26953030X-RAY DIFFRACTION91.19
2.1-2.130.30833340.2773009X-RAY DIFFRACTION92.32
2.13-2.150.29433490.26273085X-RAY DIFFRACTION92.64
2.15-2.190.28983380.24783059X-RAY DIFFRACTION94.18
2.19-2.220.26583530.24343203X-RAY DIFFRACTION95.05
2.22-2.250.26383500.23063148X-RAY DIFFRACTION95.63
2.25-2.290.24913490.21843143X-RAY DIFFRACTION96.33
2.29-2.330.26293530.21423171X-RAY DIFFRACTION96.52
2.33-2.370.25713580.21593182X-RAY DIFFRACTION96.77
2.37-2.420.26813610.20513252X-RAY DIFFRACTION97.05
2.42-2.470.2443510.19873148X-RAY DIFFRACTION96.79
2.47-2.520.22353570.20713210X-RAY DIFFRACTION97.41
2.52-2.580.233530.19073193X-RAY DIFFRACTION97.1
2.58-2.640.24483610.19093227X-RAY DIFFRACTION97.21
2.64-2.710.22553600.1923230X-RAY DIFFRACTION97.58
2.71-2.790.23173570.18553202X-RAY DIFFRACTION97.53
2.79-2.880.23973570.18693218X-RAY DIFFRACTION97.7
2.88-2.990.18933590.17863224X-RAY DIFFRACTION97.82
2.99-3.110.21563560.16653233X-RAY DIFFRACTION97.66
3.11-3.250.19863550.16653241X-RAY DIFFRACTION97.9
3.25-3.420.22053640.16973252X-RAY DIFFRACTION97.65
3.42-3.630.18583470.15393156X-RAY DIFFRACTION97.09
3.63-3.910.18883600.1473161X-RAY DIFFRACTION95.91
3.91-4.310.1623540.14363186X-RAY DIFFRACTION96.54
4.31-4.930.1833620.14923227X-RAY DIFFRACTION98.17
4.93-6.20.20183600.18053237X-RAY DIFFRACTION98.39
6.21-43.540.20893640.20113245X-RAY DIFFRACTION98.07
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)
12.55852241556-0.102955566425-0.1602985107873.983082869660.3532951061393.821793477650.006821046122660.08766247071890.0536872113093-0.3065123455940.051826398718-0.399658166932-0.08436949935030.270916332551-0.05315048493360.1859101691950.02053288687050.04283501621710.169631949001-0.005818106778410.186566641621-9.31-1.368-28.778
23.33447623214-1.93245597167-0.5479690060874.1140209271-0.5050835140952.55774853050.1500906944080.03934254758130.326395214014-0.04161026363080.0231100300003-0.0029422375239-0.570842756007-0.231031226018-0.1532982731820.3429809274050.06014384198670.05960060473360.1657735902120.009664783659240.153509019404-26.2915.897-16.824
32.35102695098-0.231923253263-0.4201843674973.963921033070.0602051037572.96408502691-0.0254744076676-0.1894732865740.02324428532640.5260330239570.0536368288097-0.07666050461550.1545715518450.0341285132534-0.0271122547660.2193946593170.0133109044488-0.03397905865930.155080897465-0.01581958813350.129619034982-19.241-7.7884.31
43.002672078132.157004649641.208718765143.845851214711.245869169442.74741515914-0.00519277325440.0693266475879-0.250981544764-0.03761748510010.00850212232195-0.0813669624530.420068221091-0.0648686702492-0.001138274112630.245690724826-0.01447250948580.02793959112860.130385492898-0.003705368017820.13236056122-23.908-25.499-15.463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 45:221 )B45 - 221
2X-RAY DIFFRACTION2( CHAIN B AND RESID 222:357 )B222 - 357
3X-RAY DIFFRACTION3( CHAIN A AND RESID 42:200 )A42 - 200
4X-RAY DIFFRACTION4( CHAIN A AND RESID 201:357 )A201 - 357

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