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- PDB-3eat: Crystal structure of the PvcB (PA2255) protein from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 3eat
TitleCrystal structure of the PvcB (PA2255) protein from Pseudomonas aeruginosa
ComponentsPyoverdine biosynthesis protein PvcB
KeywordsOXIDOREDUCTASE / PvcB / paerucumarin / Fe/alpha-ketoglutarate dependent hydroxylase / 2-isocyano-6 / 7-dihydroxycoumarin
Function / homologyClavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / oxidoreductase activity / Alpha Beta / Paerucumarin biosynthesis protein PvcB
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsGulick, A.M. / Drake, E.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Three-dimensional structures of Pseudomonas aeruginosa PvcA and PvcB, two proteins involved in the synthesis of 2-isocyano-6,7-dihydroxycoumarin.
Authors: Drake, E.J. / Gulick, A.M.
History
DepositionAug 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Pyoverdine biosynthesis protein PvcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4042
Polymers33,3811
Non-polymers231
Water2,162120
1
X: Pyoverdine biosynthesis protein PvcB
hetero molecules

X: Pyoverdine biosynthesis protein PvcB
hetero molecules

X: Pyoverdine biosynthesis protein PvcB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2136
Polymers100,1443
Non-polymers693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area5410 Å2
ΔGint-31 kcal/mol
Surface area34330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.350, 125.350, 107.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11X-304-

NA

21X-422-

HOH

31X-423-

HOH

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Components

#1: Protein Pyoverdine biosynthesis protein PvcB


Mass: 33381.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: pvcB, PA2255 / Plasmid: pET15bTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I1L4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.64 Å3/Da / Density % sol: 66.19 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2-5% PEG 20000, 75-150 mM NaCitrate, 100 mM BTP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 17774 / Num. obs: 17734 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.1
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SnBphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.244 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 918 5.2 %RANDOM
Rwork0.187 ---
obs0.189 16728 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.888 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å2-0.95 Å20 Å2
2---1.91 Å20 Å2
3---2.86 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 1 120 2350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212297
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9423119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9521.557122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1515345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4551529
X-RAY DIFFRACTIONr_chiral_restr0.0870.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021840
X-RAY DIFFRACTIONr_nbd_refined0.1940.2897
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21477
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3050.29
X-RAY DIFFRACTIONr_mcbond_it2.13821389
X-RAY DIFFRACTIONr_mcangle_it3.60532212
X-RAY DIFFRACTIONr_scbond_it2.2662941
X-RAY DIFFRACTIONr_scangle_it3.3533907
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 64 -
Rwork0.273 1193 -
obs--99.6 %

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