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- PDB-5i90: Crystal Structure of PvdN from Pseudomonas Aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5i90
TitleCrystal Structure of PvdN from Pseudomonas Aeruginosa
ComponentsPvdN
KeywordsTRANSFERASE / pyoverdine PLP aminotransferase
Function / homology
Function and homology information


pyoverdine biosynthetic process / outer membrane-bounded periplasmic space
Similarity search - Function
Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / PvdN
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.219 Å
AuthorsDrake, E.J. / Gulick, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116957 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: 1.2 angstrom resolution crystal structure of the periplasmic aminotransferase PvdN from Pseudomonas aeruginosa.
Authors: Drake, E.J. / Gulick, A.M.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: PvdN
B: PvdN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9049
Polymers96,0992
Non-polymers8057
Water11,926662
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-17 kcal/mol
Surface area27850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.521, 98.996, 63.046
Angle α, β, γ (deg.)90.00, 102.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PvdN


Mass: 48049.449 Da / Num. of mol.: 2 / Mutation: N2D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pvdN, PA2394 / Production host: Escherichia coli (E. coli) / References: UniProt: G3XCY5
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / 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: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10-14% PEG 8000, 100-200 mM Glycine, 50 mM MES (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 15, 2011 / Details: Si(111) and Si(220) double crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.219→29.407 Å / Num. obs: 221938 / % possible obs: 99.88 % / Redundancy: 4.6 % / Net I/σ(I): 22.92
Reflection shellResolution: 1.219→1.263 Å / Redundancy: 3.6 % / % possible all: 98.99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
Cootmodel building
ARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.219→29.407 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1583 11141 5.02 %
Rwork0.1396 --
obs0.1405 221908 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.219→29.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6251 0 52 662 6965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066651
X-RAY DIFFRACTIONf_angle_d0.8759041
X-RAY DIFFRACTIONf_dihedral_angle_d16.1392479
X-RAY DIFFRACTIONf_chiral_restr0.079964
X-RAY DIFFRACTIONf_plane_restr0.0051195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2194-1.23320.24013540.20886836X-RAY DIFFRACTION97
1.2332-1.24780.19623900.19456966X-RAY DIFFRACTION100
1.2478-1.2630.18873450.1877033X-RAY DIFFRACTION100
1.263-1.2790.18553370.17157017X-RAY DIFFRACTION100
1.279-1.29580.21263780.1676999X-RAY DIFFRACTION100
1.2958-1.31350.18343390.15757100X-RAY DIFFRACTION100
1.3135-1.33230.16453480.1467037X-RAY DIFFRACTION100
1.3323-1.35220.16953910.13996956X-RAY DIFFRACTION100
1.3522-1.37330.16143650.13517045X-RAY DIFFRACTION100
1.3733-1.39580.15523920.13047019X-RAY DIFFRACTION100
1.3958-1.41990.15733790.12576991X-RAY DIFFRACTION100
1.4199-1.44570.14733510.1237005X-RAY DIFFRACTION100
1.4457-1.47350.14333650.1187040X-RAY DIFFRACTION100
1.4735-1.50360.15553930.11387051X-RAY DIFFRACTION100
1.5036-1.53630.13214110.10916951X-RAY DIFFRACTION100
1.5363-1.5720.14453800.10727023X-RAY DIFFRACTION100
1.572-1.61130.13634080.10587000X-RAY DIFFRACTION100
1.6113-1.65490.14123680.10587013X-RAY DIFFRACTION100
1.6549-1.70360.13813820.10937035X-RAY DIFFRACTION100
1.7036-1.75860.13373510.11417047X-RAY DIFFRACTION100
1.7586-1.82140.13553500.11617022X-RAY DIFFRACTION100
1.8214-1.89430.1384250.12267015X-RAY DIFFRACTION100
1.8943-1.98050.14793680.12677033X-RAY DIFFRACTION100
1.9805-2.08490.14363520.12887071X-RAY DIFFRACTION100
2.0849-2.21550.15143760.13297041X-RAY DIFFRACTION100
2.2155-2.38650.15933500.13787079X-RAY DIFFRACTION100
2.3865-2.62650.16653620.15147077X-RAY DIFFRACTION100
2.6265-3.00630.17843820.15827057X-RAY DIFFRACTION100
3.0063-3.78630.17393440.15467088X-RAY DIFFRACTION100
3.7863-29.41590.15444050.14727120X-RAY DIFFRACTION100

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