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- PDB-6e13: Pseudomonas putida PqqB with a non-physiological zinc at the acti... -

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Basic information

Entry
Database: PDB / ID: 60000000000000
TitlePseudomonas putida PqqB with a non-physiological zinc at the active site binds the substrate mimic, 5-cysteinyl-3,4-dihydroxyphenylalanine (5-Cys-DOPA), non-specifically but supports the proposed function of the enzyme in pyrroloquinoline quinone biosynthesis.
ComponentsCoenzyme PQQ synthesis protein B
KeywordsOXIDOREDUCTASE / iron-dependent / hydroxylase / metallo beta-lactamase
Function / homology
Function and homology information


pyrroloquinoline quinone biosynthetic process
Similarity search - Function
Coenzyme PQQ biosynthesis protein B / Beta-lactamase superfamily domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HKS / Coenzyme PQQ synthesis protein B
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.349 Å
AuthorsEvans III, R.L. / Wilmot, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-66569 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-118117 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Discovery of Hydroxylase Activity for PqqB Provides a Missing Link in the Pyrroloquinoline Quinone Biosynthetic Pathway.
Authors: Koehn, E.M. / Latham, J.A. / Armand, T. / Evans 3rd, R.L. / Tu, X. / Wilmot, C.M. / Iavarone, A.T. / Klinman, J.P.
History
DepositionJul 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coenzyme PQQ synthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4825
Polymers34,0001
Non-polymers4834
Water55831
1
A: Coenzyme PQQ synthesis protein B
hetero molecules

A: Coenzyme PQQ synthesis protein B
hetero molecules


  • defined by author&software
  • Evidence: light scattering, Dynamic light scattering and size exclusion chromatography were used to confirm the homodimer. Also, this structure (Pseudomonas putida PqqB and Methylobacterium ...Evidence: light scattering, Dynamic light scattering and size exclusion chromatography were used to confirm the homodimer. Also, this structure (Pseudomonas putida PqqB and Methylobacterium extorquens PqqB) has been previously deposited as a homodimer (see PDB IDs 4Z6X, 4Z67, 4Z5Y, 4Z5Z, 4Z60, 4Z7r, etc...).
  • 69 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)68,96410
Polymers67,9992
Non-polymers9658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4970 Å2
ΔGint-119 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.038, 86.038, 107.128
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

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Components

#1: Protein Coenzyme PQQ synthesis protein B / Pyrroloquinoline quinone biosynthesis protein B


Mass: 33999.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria)
Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: pqqB, PP_0379 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88QV5, Oxidoreductases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HKS / 3-{[(2S)-2-amino-2-carboxyethyl]sulfanyl}-5-hydroxy-L-tyrosine / 5-cysteinyl-3,4-dihydroxyphenylalanine / 5-Cys-DOPA


Mass: 316.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N2O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 2.5 mg/mL PqqB, 50 mM sodium chloride, 10 mM Tris-HCl, pH 7.5 against reservoir solution for unliganded PqqB (11% PEG4000, 0.2 M sodium chloride, 80 uM zinc chloride, 0.1 M Bis-Tris, pH 6.7)

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2015
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 17434 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.037 / Rrim(I) all: 0.13 / Χ2: 1.072 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.3912.20.9278640.8590.2740.9671.043100
2.39-2.4312.10.7878370.8810.2340.8211.076100
2.43-2.4812.20.7478500.8980.2210.7791.054100
2.48-2.5312.20.6648650.9080.1970.6931.055100
2.53-2.5912.10.5768390.9290.1710.6011.081100
2.59-2.6512.10.488590.9350.1430.5011.072100
2.65-2.7112.10.4538500.9520.1350.4731.091100
2.71-2.7912.10.3658590.9640.1080.3811.077100
2.79-2.8712.10.3088570.9720.0910.3211.087100
2.87-2.9612.10.2498580.9820.0740.261.083100
2.96-3.0712.10.2148690.9850.0640.2241.069100
3.07-3.1912.10.1798530.9920.0530.1871.071100
3.19-3.3312.10.148610.9940.0420.1471.06100
3.33-3.5112.10.1098680.9950.0330.1141.109100
3.51-3.73120.1048870.9950.0310.1081.095100
3.73-4.02120.0968600.9960.0290.11.068100
4.02-4.4211.90.0798940.9970.0230.0821.087100
4.42-5.0611.70.0679050.9970.020.071.047100
5.06-6.3711.50.0679010.9980.020.071.02100
6.37-5010.60.0639980.9970.020.0661.09499.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementResolution: 2.349→45.472 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 929 5.34 %
Rwork0.1893 16455 -
obs0.1917 17384 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.7 Å2 / Biso mean: 44.0654 Å2 / Biso min: 18.94 Å2
Refinement stepCycle: final / Resolution: 2.349→45.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 24 31 2436
Biso mean--49.99 37.86 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072471
X-RAY DIFFRACTIONf_angle_d0.9793358
X-RAY DIFFRACTIONf_chiral_restr0.054361
X-RAY DIFFRACTIONf_plane_restr0.006449
X-RAY DIFFRACTIONf_dihedral_angle_d14.9232036
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3489-2.47280.31491410.248722882429
2.4728-2.62770.23271390.222922872426
2.6277-2.83050.2881380.217823092447
2.8305-3.11530.26681170.205723392456
3.1153-3.5660.27351400.194623322472
3.566-4.49210.16941190.162923862505
4.4921-45.48040.22341350.177525142649

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