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- PDB-4ylm: Structure of PvcB, an Fe, alpha-ketoglutarate dependent oxygenase... -

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Basic information

Entry
Database: PDB / ID: 4ylm
TitleStructure of PvcB, an Fe, alpha-ketoglutarate dependent oxygenase from an isonitrile synthetic pathway
ComponentsPyoverdine biosynthesis protein PvcB
KeywordsOXIDOREDUCTASE / oxygenase / Fe/a-ketoglutarate
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyoverdine biosynthesis protein PvcB / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZhu, J. / Lippa, G.M. / Gulick, A.M. / Tipton, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1158169 United States
CitationJournal: Biochemistry / Year: 2015
Title: Examining Reaction Specificity in PvcB, a Source of Diversity in Isonitrile-Containing Natural Products.
Authors: Zhu, J. / Lippa, G.M. / Gulick, A.M. / Tipton, P.A.
History
DepositionMar 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)33,6584
Polymers33,3811
Non-polymers2763
Water2,702150
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)100,97312
Polymers100,1443
Non-polymers8299
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7590 Å2
ΔGint-16 kcal/mol
Surface area33330 Å2
MethodPISA
2
X: Pyoverdine biosynthesis protein PvcB
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)201,94724
Polymers200,2896
Non-polymers1,65818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area19500 Å2
ΔGint-69 kcal/mol
Surface area62330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.950, 124.950, 107.210
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-463-

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 (PAK) (bacteria)
Strain: PAK / Gene: PAK_03057, Y880_0112155 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: S0I3V6, UniProt: A0A0M3KL23*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M BTP pH 7.5, 5% PEG 20000, 0.1 M sodium citrate tribasic

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0323 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0323 Å / Relative weight: 1
ReflectionResolution: 2.02→40.9 Å / Num. all: 32890 / Num. obs: 32890 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 12.6
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EAT

3eat


Resolution: 2.05→40.9 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 1606 5.1 %RANDOM
Rwork0.1873 ---
obs0.1889 31489 99.96 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.293 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.9146 Å2-0 Å20 Å2
2---5.9146 Å2-0 Å2
3---11.8292 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 18 150 2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072291
X-RAY DIFFRACTIONf_angle_d1.0553108
X-RAY DIFFRACTIONf_dihedral_angle_d13.934840
X-RAY DIFFRACTIONf_chiral_restr0.085316
X-RAY DIFFRACTIONf_plane_restr0.005414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11620.22181630.21032643X-RAY DIFFRACTION100
2.1162-2.19180.25531230.1982689X-RAY DIFFRACTION100
2.1918-2.27960.22761400.1952664X-RAY DIFFRACTION100
2.2796-2.38330.26131250.18842684X-RAY DIFFRACTION100
2.3833-2.5090.22881500.19662672X-RAY DIFFRACTION100
2.509-2.66610.21921230.1892711X-RAY DIFFRACTION100
2.6661-2.87190.23281590.19472688X-RAY DIFFRACTION100
2.8719-3.16080.19821590.19042701X-RAY DIFFRACTION100
3.1608-3.6180.20161550.18352720X-RAY DIFFRACTION100
3.618-4.55730.19591460.16482778X-RAY DIFFRACTION100
4.5573-40.90.24011630.19792933X-RAY DIFFRACTION100

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