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- PDB-9ooz: Crystal structure of PqqT Y161W Variant with PQQ bound -

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Basic information

Entry
Database: PDB / ID: 9ooz
TitleCrystal structure of PqqT Y161W Variant with PQQ bound
ComponentsABC transporter substrate binding protein (Subunit A)
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 / ABC transporter substrate binding protein (Subunit A)
Function and homology information
Biological speciesMethylorubrum extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsBruchs, A.T. / Thompson, P.J. / Nava-Matadamas, C. / Mohd, T. / Olshansky, L. / Bridwell-Rabb, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138138 United States
Department of Energy (DOE, United States)DE-SC0021240 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Mechanistic Interrogation of a PQQ and Rare Earth-Dependent Artificial Metalloenzyme.
Authors: Taher, M. / Thompson, P.J. / Nava-Matadamas, C. / Bruchs, A.T. / Bridwell-Rabb, J. / Olshansky, L.
History
DepositionMay 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter substrate binding protein (Subunit A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3227
Polymers32,8141
Non-polymers5076
Water2,630146
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)53.518, 118.695, 40.343
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein ABC transporter substrate binding protein (Subunit A) / ABC transporter substrate-binding protein


Mass: 32814.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens (bacteria) / Gene: KEC54_10240, TK0001_4169 / Variant: Y161W / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1P8QVR7
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.84 Å3/Da / Density % sol: 33.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30 mM MOPS pH 7.0, 100 mM NaCl, 80 mM citric acid pH 3.8, 3.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→40 Å / Num. obs: 17479 / % possible obs: 94 % / Redundancy: 10.93 % / Biso Wilson estimate: 31.9 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.073 / Net I/σ(I): 23.46
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 5.73 % / Mean I/σ(I) obs: 3.51 / Num. unique obs: 1560 / CC1/2: 0.886 / Rrim(I) all: 0.514 / % possible all: 89.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→38.2 Å / SU ML: 0.2271 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.7692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2134 875 5.01 %
Rwork0.1953 16604 -
obs0.1962 17479 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.63 Å2
Refinement stepCycle: LAST / Resolution: 1.98→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2225 0 29 146 2400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01162330
X-RAY DIFFRACTIONf_angle_d1.36513168
X-RAY DIFFRACTIONf_chiral_restr0.077348
X-RAY DIFFRACTIONf_plane_restr0.0165419
X-RAY DIFFRACTIONf_dihedral_angle_d12.3894837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.10.31671360.25712572X-RAY DIFFRACTION89.61
2.1-2.270.26971330.22162531X-RAY DIFFRACTION87.8
2.27-2.490.25761530.20722917X-RAY DIFFRACTION99.97
2.49-2.860.21491430.19962718X-RAY DIFFRACTION93.07
2.86-3.590.20051520.19742883X-RAY DIFFRACTION97.43
3.6-38.20.18771580.17742983X-RAY DIFFRACTION96.03

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