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- PDB-9b1u: Crystal structure of PqqT with PQQ bound -

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Basic information

Entry
Database: PDB / ID: 9b1u
TitleCrystal structure of PqqT with PQQ 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 / PYRROLOQUINOLINE QUINONE / Putative ABC transporter periplasmic solute-binding protein
Function and homology information
Biological speciesMethylorubrum extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsBoggs, D. / Bruchs, A. / Thompson, P. / 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)33,1674
Polymers32,7911
Non-polymers3763
Water4,432246
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)40.004, 53.191, 119.068
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 (strain CM4 / NCIMB 13688) (bacteria)
Strain: CM4 / NCIMB 13688 / Gene: Mchl_2142 / Production host: Escherichia coli (E. coli) / References: UniProt: B7KXB5
#2: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 1.93 Å3/Da / Density % sol: 36.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 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: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.46→40 Å / Num. obs: 42803 / % possible obs: 94.9 % / Redundancy: 12.53 % / Biso Wilson estimate: 19.46 Å2 / CC1/2: 1 / Rrim(I) all: 0.052 / Net I/σ(I): 26.57
Reflection shellResolution: 1.46→1.55 Å / Redundancy: 9.37 % / Num. unique obs: 5315 / Rrim(I) all: 0.46 / % possible all: 73.8

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Processing

Software
NameVersionClassification
XDS20230630data reduction
XDS20230630data scaling
PHENIX1.21-5207phasing
Coot0.9.8.92model building
PHENIX1.21-5207refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→37.92 Å / SU ML: 0.1563 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2071 2139 5 %
Rwork0.1987 40618 -
obs0.1991 42757 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.21 Å2
Refinement stepCycle: LAST / Resolution: 1.46→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 26 246 2495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01392519
X-RAY DIFFRACTIONf_angle_d1.58863435
X-RAY DIFFRACTIONf_chiral_restr0.0906377
X-RAY DIFFRACTIONf_plane_restr0.0196459
X-RAY DIFFRACTIONf_dihedral_angle_d12.1125916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.275990.26991882X-RAY DIFFRACTION66.61
1.49-1.530.24991120.24272139X-RAY DIFFRACTION76.31
1.53-1.570.26871280.23932437X-RAY DIFFRACTION87.1
1.57-1.620.25861470.2262781X-RAY DIFFRACTION98.82
1.62-1.670.23251510.23492847X-RAY DIFFRACTION100
1.67-1.730.23451460.2312784X-RAY DIFFRACTION99.8
1.73-1.80.24261480.21632814X-RAY DIFFRACTION99.53
1.8-1.880.28561490.21522814X-RAY DIFFRACTION99.46
1.88-1.980.21971450.21222764X-RAY DIFFRACTION97.55
1.98-2.110.21651500.21332854X-RAY DIFFRACTION99.97
2.11-2.270.20981490.20282825X-RAY DIFFRACTION100
2.27-2.50.2131520.20162881X-RAY DIFFRACTION99.84
2.5-2.860.21411490.19582846X-RAY DIFFRACTION98.39
2.86-3.60.17221530.18462901X-RAY DIFFRACTION99.77
3.6-37.920.19081610.18133049X-RAY DIFFRACTION99.14

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