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- PDB-8ebg: Crystal structure of the probable FhuD FeIII-dicitrate-binding do... -

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Basic information

Entry
Database: PDB / ID: 8ebg
TitleCrystal structure of the probable FhuD FeIII-dicitrate-binding domain protein FecB from Mycobacterium tuberculosis
ComponentsFEIII-dicitrate-binding periplasmic lipoprotein FecB
KeywordsUNKNOWN FUNCTION / siderophore binding protein / siderophore / Structural Genomics / Midwest Center for Structural Genomics / MCSG / Metal binding protein / PSI-Biology
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. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FORMIC ACID / Probable FEIII-dicitrate-binding periplasmic lipoprotein FecB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.43 Å
AuthorsCuff, M. / Kim, Y. / Endres, M. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of the probable FhuD FeIII-dicitrate-binding domain protein FecB from Mycobacterium tuberculosis
Authors: Cuff, M. / Kim, Y. / Endres, M. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionAug 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,4877
Polymers70,1052
Non-polymers3825
Water12,881715
1
A: FEIII-dicitrate-binding periplasmic lipoprotein FecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1913
Polymers35,0521
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FEIII-dicitrate-binding periplasmic lipoprotein FecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2974
Polymers35,0521
Non-polymers2443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.631, 76.517, 79.076
Angle α, β, γ (deg.)90.000, 102.500, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 35052.492 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 BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: O53291
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17 M Ammonium acetate, 0.085 M sodium citrate pH 5.6, 25.5 % (w/v) PEG4000, 15 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 116192 / % possible obs: 95.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.06 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.058 / Net I/σ(I): 28.9
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2 / Num. unique obs: 4188 / CC1/2: 0.753 / Rpim(I) all: 0.032 / Rrim(I) all: 0.066 / % possible all: 69.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.43→28.85 Å / SU ML: 0.121 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.8335
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1704 5643 4.86 %
Rwork0.1414 110498 -
obs0.1428 116141 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.04 Å2
Refinement stepCycle: LAST / Resolution: 1.43→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 25 715 5426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00885129
X-RAY DIFFRACTIONf_angle_d0.97117069
X-RAY DIFFRACTIONf_chiral_restr0.0867804
X-RAY DIFFRACTIONf_plane_restr0.0093975
X-RAY DIFFRACTIONf_dihedral_angle_d11.64861844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.440.25911130.21672615X-RAY DIFFRACTION66.49
1.44-1.460.22751430.19782822X-RAY DIFFRACTION74.2
1.46-1.480.26081540.18763149X-RAY DIFFRACTION82.31
1.48-1.50.20621790.17183488X-RAY DIFFRACTION90.08
1.5-1.520.191920.15733562X-RAY DIFFRACTION93.43
1.52-1.540.18641960.1453639X-RAY DIFFRACTION94.6
1.54-1.560.19532040.14173696X-RAY DIFFRACTION95.75
1.56-1.580.1711960.14183661X-RAY DIFFRACTION95.71
1.58-1.610.20261960.13653711X-RAY DIFFRACTION96.49
1.61-1.640.16981870.12943713X-RAY DIFFRACTION97.14
1.64-1.660.19841920.12343779X-RAY DIFFRACTION96.88
1.66-1.690.16811920.12053750X-RAY DIFFRACTION98.26
1.69-1.730.16612030.11353754X-RAY DIFFRACTION97.63
1.73-1.760.15921930.11133796X-RAY DIFFRACTION98.45
1.76-1.80.16041790.11553800X-RAY DIFFRACTION98.3
1.8-1.840.16342000.12383792X-RAY DIFFRACTION98.25
1.84-1.890.15562180.1323783X-RAY DIFFRACTION98.62
1.89-1.940.15271970.12893801X-RAY DIFFRACTION99.35
1.94-20.16191860.12613833X-RAY DIFFRACTION98.99
2-2.060.1681840.13213841X-RAY DIFFRACTION99.24
2.06-2.130.16551760.13273863X-RAY DIFFRACTION99.34
2.13-2.220.15182040.1283812X-RAY DIFFRACTION99.41
2.22-2.320.19121810.13413893X-RAY DIFFRACTION99.56
2.32-2.440.1561870.13593848X-RAY DIFFRACTION99.61
2.44-2.60.1771800.14643866X-RAY DIFFRACTION99.7
2.6-2.80.17211940.15083892X-RAY DIFFRACTION99.85
2.8-3.080.1782050.1573863X-RAY DIFFRACTION99.75
3.08-3.520.18252230.15513868X-RAY DIFFRACTION99.83
3.52-4.430.15041840.13993856X-RAY DIFFRACTION98.56
4.43-28.850.16592050.15073752X-RAY DIFFRACTION94.78

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