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- PDB-3jxp: Crystal Structure of the Coenzyme PQQ Synthesis Protein (PqqB) fr... -

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Basic information

Entry
Database: PDB / ID: 3jxp
TitleCrystal Structure of the Coenzyme PQQ Synthesis Protein (PqqB) from Pseudomonas putida
ComponentsCoenzyme PQQ synthesis protein B
KeywordsBIOSYNTHETIC PROTEIN / alpha-beta protein / pqq biosynthesis / Transport
Function / homology
Function and homology information


pyrroloquinoline quinone biosynthetic process
Similarity search - Function
Coenzyme PQQ biosynthesis protein B / Beta-lactamase superfamily domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Coenzyme PQQ synthesis protein B
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMetlitzky, M. / Schwarzenbacher, R.
CitationJournal: J. Biophys. Chem. / Year: 2012
Title: Crystal structure of PqqB from Pseudomonas putida at 2.2 A resolution
Authors: Metlitzky, M. / Puehringer, S. / Fisher, S.J.
History
DepositionSep 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 16, 2013Group: Database references
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coenzyme PQQ synthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8774
Polymers35,7401
Non-polymers1363
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Coenzyme PQQ synthesis protein B
hetero molecules

A: Coenzyme PQQ synthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7538
Polymers71,4812
Non-polymers2736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5220 Å2
ΔGint-75 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.209, 86.209, 109.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsmonomer

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Components

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


Mass: 35740.426 Da / Num. of mol.: 1 / Mutation: M253T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP_0379, pqqB / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(de3)Star / References: UniProt: Q88QV5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS hydrochloride pH 8.5, 0.2 M Magnesium chloride hexahydrate, 15% w/v PEG 4,000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 18, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→67.7 Å / Num. all: 21579 / Num. obs: 21411 / % possible obs: 98.2 %
Reflection shellResolution: 2.2→2.257 Å / Rmerge(I) obs: 0.569 / % possible all: 99.62

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XTO

1xto


Resolution: 2.2→67.7 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.926 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24348 1065 5 %RANDOM
Rwork0.19757 ---
obs0.19988 20344 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.329 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.2→67.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 3 174 2519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212408
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9553273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12424115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75915387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9971519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021876
X-RAY DIFFRACTIONr_nbd_refined0.2050.21026
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2201
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.460.238
X-RAY DIFFRACTIONr_mcbond_it1.041.51550
X-RAY DIFFRACTIONr_mcangle_it1.72422424
X-RAY DIFFRACTIONr_scbond_it2.5153965
X-RAY DIFFRACTIONr_scangle_it3.7684.5847
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 76 -
Rwork0.219 1481 -
obs--99.62 %

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