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- PDB-6eyv: Crystal structure of the pyoverdine maturation protein PvdP in co... -

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Basic information

Entry
Database: PDB / ID: 6eyv
TitleCrystal structure of the pyoverdine maturation protein PvdP in complex with the mock substrates L-tyrosine and zinc.
ComponentsPvdP
KeywordsOXIDOREDUCTASE / tyrosinase / pyoverdine / barrel / zinc
Function / homologyDi-copper centre-containing domain superfamily / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / TYROSINE / PvdP
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å
AuthorsPoppe, J. / Blankenfeldt, W.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Pseudomonas aeruginosapyoverdine maturation enzyme PvdP has a noncanonical domain architecture and affords insight into a new subclass of tyrosinases.
Authors: Poppe, J. / Reichelt, J. / Blankenfeldt, W.
History
DepositionNov 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: PvdP
A: PvdP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1408
Polymers123,5162
Non-polymers6246
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-180 kcal/mol
Surface area37510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.332, 109.143, 82.510
Angle α, β, γ (deg.)90.00, 95.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PvdP


Mass: 61758.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: pvdP, PA14_33740 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: A0A0H2ZBG1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.81 Å3/Da / Density % sol: 56.16 % / Description: thin plates
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.857 M NH4SO4 0.1 M MES pH 5.5 0.5 M ZnCl2 1 mM L-tyrosine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.282 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.701→48.092 Å / Num. obs: 23084 / % possible obs: 92.2 % / Redundancy: 9.9 % / CC1/2: 0.988 / Rpim(I) all: 0.101 / Rrim(I) all: 0.32 / Net I/σ(I): 8.6
Reflection shellResolution: 2.701→3.032 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.6 / Num. measured obs: 8710 / Num. unique obs: 1154 / CC1/2: 0.506 / Rpim(I) all: 0.536 / % possible all: 56.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2875)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EYS

6eys


Resolution: 2.704→48.092 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.55
RfactorNum. reflection% reflection
Rfree0.2618 1990 8.67 %
Rwork0.2046 --
obs0.2096 22962 61.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.704→48.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7333 0 30 24 7387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027605
X-RAY DIFFRACTIONf_angle_d0.4610361
X-RAY DIFFRACTIONf_dihedral_angle_d14.7354424
X-RAY DIFFRACTIONf_chiral_restr0.0391046
X-RAY DIFFRACTIONf_plane_restr0.0031381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7043-2.7720.34340.324245X-RAY DIFFRACTION2
2.772-2.84690.6895100.3395104X-RAY DIFFRACTION4
2.8469-2.93070.4748250.3162262X-RAY DIFFRACTION11
2.9307-3.02530.3484540.2961547X-RAY DIFFRACTION23
3.0253-3.13340.3421820.2708926X-RAY DIFFRACTION38
3.1334-3.25880.30861170.27671259X-RAY DIFFRACTION52
3.2588-3.40710.32631520.25641583X-RAY DIFFRACTION65
3.4071-3.58660.29871850.21811859X-RAY DIFFRACTION77
3.5866-3.81130.30182010.19962154X-RAY DIFFRACTION89
3.8113-4.10540.23142300.18112408X-RAY DIFFRACTION99
4.1054-4.51830.21542260.17442444X-RAY DIFFRACTION100
4.5183-5.17140.21432440.17382437X-RAY DIFFRACTION100
5.1714-6.51280.24722330.20682448X-RAY DIFFRACTION100
6.5128-48.09920.27152270.21012496X-RAY DIFFRACTION100

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