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- PDB-9b1v: Crystal structure of PqqT with PQQ and Gd3+ bound -

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Basic information

Entry
Database: PDB / ID: 9b1v
TitleCrystal structure of PqqT with PQQ and Gd3+ bound
ComponentsPutative ABC transporter periplasmic solute-binding protein
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein
Function / homologySsuA/THI5-like / NMT1/THI5 like / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / GADOLINIUM ION / PYRROLOQUINOLINE QUINONE / Putative ABC transporter periplasmic solute-binding protein
Function and homology information
Biological speciesMethylorubrum extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBoggs, G.D. / Bruchs, A.T. / Thompson, P.J. / Olshansky, L. / Bridwell-Rabb, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138138 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structure-driven development of a biomimetic rare earth artificial metalloprotein.
Authors: Thompson, P.J. / Boggs, D.G. / Wilson, C.A. / Bruchs, A.T. / Velidandla, U. / Bridwell-Rabb, J. / Olshansky, L.
History
DepositionMar 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ABC transporter periplasmic solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7798
Polymers32,7911
Non-polymers9887
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.867, 53.389, 119.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Putative ABC transporter periplasmic solute-binding protein


Mass: 32791.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (bacteria) / Gene: Mchl_2142 / Production host: Escherichia coli (E. coli) / References: UniProt: B7KXB5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GD3 / GADOLINIUM ION


Mass: 157.250 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Gd / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 1.94 Å3/Da / Density % sol: 36.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.5 mM PQQ, 20 mM NaCl, 20 mM HEPES pH 7.5, 100 mM citric acid pH 3.8 and 3.0 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.3776 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3776 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. obs: 69177 / % possible obs: 96.9 % / Redundancy: 5.73 % / Biso Wilson estimate: 17.96 Å2 / CC1/2: 0.995 / Net I/σ(I): 12.73
Reflection shellResolution: 1.55→1.64 Å / Num. unique obs: 9386 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20230630data reduction
XDS20230630data scaling
PHENIX1.21-5207phasing
Coot0.9.8.92model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→39.81 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.5496
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1862 3462 5.01 %
Rwork0.1779 65673 -
obs0.1784 69135 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.69 Å2
Refinement stepCycle: LAST / Resolution: 1.55→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 39 236 2494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01442529
X-RAY DIFFRACTIONf_angle_d1.59923447
X-RAY DIFFRACTIONf_chiral_restr0.0934378
X-RAY DIFFRACTIONf_plane_restr0.0175461
X-RAY DIFFRACTIONf_dihedral_angle_d12.3804919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.27970.22541847X-RAY DIFFRACTION68.35
1.57-1.590.23481120.21592113X-RAY DIFFRACTION77.5
1.59-1.620.21881230.21092317X-RAY DIFFRACTION86.59
1.62-1.640.23721330.20662545X-RAY DIFFRACTION94.8
1.64-1.670.25441430.20762685X-RAY DIFFRACTION96.16
1.67-1.70.21051410.20062657X-RAY DIFFRACTION99.64
1.7-1.730.22771380.21032708X-RAY DIFFRACTION99.96
1.73-1.760.18061430.19092704X-RAY DIFFRACTION99.93
1.76-1.80.22681430.19622750X-RAY DIFFRACTION99.97
1.8-1.840.19981450.20212719X-RAY DIFFRACTION100
1.84-1.880.22351390.19012676X-RAY DIFFRACTION100
1.88-1.930.21430.19832688X-RAY DIFFRACTION99.96
1.93-1.980.19161430.18562762X-RAY DIFFRACTION99.93
1.98-2.040.2131430.18262701X-RAY DIFFRACTION99.96
2.04-2.10.18651410.18612725X-RAY DIFFRACTION99.97
2.1-2.180.17091420.18312682X-RAY DIFFRACTION100
2.18-2.270.21491400.18032717X-RAY DIFFRACTION100
2.27-2.370.21661420.17842716X-RAY DIFFRACTION99.93
2.37-2.50.19871490.17582715X-RAY DIFFRACTION99.93
2.5-2.650.22051420.18252726X-RAY DIFFRACTION99.97
2.65-2.860.15831410.17792699X-RAY DIFFRACTION99.75
2.86-3.140.18121390.17942715X-RAY DIFFRACTION99.96
3.14-3.60.18231440.16142711X-RAY DIFFRACTION100
3.6-4.530.14631410.14722702X-RAY DIFFRACTION99.89
4.53-39.810.15941550.1772693X-RAY DIFFRACTION99.41

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