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- PDB-5hh9: Structure of PvdN from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5hh9
TitleStructure of PvdN from Pseudomonas aeruginosa
ComponentsPvdN
KeywordsTRANSFERASE / L-Cystine Desulfurase / pyoverdine
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 PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.47 Å
AuthorsXia, H. / Bai, G. / Liu, S. / Li, N. / Xu, S. / Chen, K. / Yao, Q. / Gu, L.
CitationJournal: To Be Published
Title: Structural and Biochemical Characterization of a Novel L-Cystine Desulfurase involved in the biosynthesis of the major siderophore pyoverdine in Pseudomonas aeruginosa
Authors: Xia, H. / Bai, G. / Liu, S. / Li, N. / Xu, S. / Chen, K. / Yao, Q. / Gu, L.
History
DepositionJan 10, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Structure summary
Revision 1.2Mar 20, 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

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Assembly

Deposited unit
A: PvdN
B: PvdN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0294
Polymers88,5342
Non-polymers4942
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-31 kcal/mol
Surface area27350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.654, 91.297, 61.664
Angle α, β, γ (deg.)90.00, 101.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PvdN / L-Cystine Desulfurase


Mass: 44267.137 Da / Num. of mol.: 2 / Fragment: UNP residues 38-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: pvdN / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 1.89 Å3/Da / Density % sol: 34.98 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5 / Details: 20% PEG3350, 100mM Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 109160 / % possible obs: 99.7 % / Redundancy: 3.3 % / Net I/σ(I): 23.8

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2090: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementResolution: 1.47→32.83 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1648 1989 1.82 %
Rwork0.1339 --
obs0.1345 109117 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→32.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6254 0 32 509 6795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096442
X-RAY DIFFRACTIONf_angle_d1.2398738
X-RAY DIFFRACTIONf_dihedral_angle_d16.8362378
X-RAY DIFFRACTIONf_chiral_restr0.081938
X-RAY DIFFRACTIONf_plane_restr0.0061144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4699-1.50670.24121340.17257464X-RAY DIFFRACTION96
1.5067-1.54740.20211500.1467812X-RAY DIFFRACTION100
1.5474-1.59290.22691440.13737771X-RAY DIFFRACTION99
1.5929-1.64440.17541450.12597763X-RAY DIFFRACTION99
1.6444-1.70310.17161420.11527681X-RAY DIFFRACTION99
1.7031-1.77130.16671450.10867731X-RAY DIFFRACTION99
1.7713-1.85190.14211480.10727672X-RAY DIFFRACTION98
1.8519-1.94960.16211400.10387620X-RAY DIFFRACTION97
1.9496-2.07170.13881410.10987583X-RAY DIFFRACTION97
2.0717-2.23160.15591400.11357528X-RAY DIFFRACTION96
2.2316-2.45610.16961370.12317479X-RAY DIFFRACTION95
2.4561-2.81140.14931360.13417483X-RAY DIFFRACTION95
2.8114-3.54130.15411430.14347756X-RAY DIFFRACTION98
3.5413-32.83830.17561440.15877785X-RAY DIFFRACTION98

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