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- PDB-1t9m: X-ray crystal structure of phzG from pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 1t9m
TitleX-ray crystal structure of phzG from pseudomonas aeruginosa
Componentsprobable pyridoxamine 5'-phosphate oxidase
KeywordsOXIDOREDUCTASE / phenazine / phzG / chorismate / pseudomonas
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH2 group of donors / pyridoxal 5'-phosphate synthase / phenazine biosynthetic process / pyridoxamine phosphate oxidase activity / pyridoxine biosynthetic process / FMN binding
Similarity search - Function
Pyridoxamine 5'-phosphate oxidase, conserved site / Pyridoxamine 5'-phosphate oxidase signature. / Pyridoxine 5'-phosphate oxidase, dimerisation, C-terminal / Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region / Pyridoxamine 5'-phosphate oxidase / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel ...Pyridoxamine 5'-phosphate oxidase, conserved site / Pyridoxamine 5'-phosphate oxidase signature. / Pyridoxine 5'-phosphate oxidase, dimerisation, C-terminal / Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region / Pyridoxamine 5'-phosphate oxidase / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / FLAVIN MONONUCLEOTIDE / Phenazine biosynthesis protein PhzG
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsParsons, J.F. / Eisenstein, E. / Ladner, J.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the phenazine biosynthesis enzyme PhzG.
Authors: Parsons, J.F. / Calabrese, K. / Eisenstein, E. / Ladner, J.E.
History
DepositionMay 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN FMN 250 IS ASSOCIATED WITH CHAIN A. FMN 350 IS ASSOCIATED WITH CHAIN B.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: probable pyridoxamine 5'-phosphate oxidase
B: probable pyridoxamine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,01810
Polymers48,6002
Non-polymers1,4178
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-68 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.590, 69.020, 89.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer and the dimer is contained in an asymmetric unit.

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Components

#1: Protein probable pyridoxamine 5'-phosphate oxidase


Mass: 24300.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: phzG / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: O69755
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M lithium sulfate, 0.1M tris, 25% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 21, 2003 / Details: MSC BLUE CONFOCAL OPTICS
RadiationMonochromator: MSC BLUE CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→54 Å / Num. obs: 31579 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 19
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 5.3 / Num. unique all: 5984 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1DNL

1dnl


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.463 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23103 1576 5 %RANDOM
Rwork0.1836 ---
obs0.18604 29938 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.574 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2--0.86 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 82 371 3749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0213470
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.9754726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7295406
X-RAY DIFFRACTIONr_chiral_restr0.1620.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022746
X-RAY DIFFRACTIONr_nbd_refined0.2120.21513
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2316
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.213
X-RAY DIFFRACTIONr_mcbond_it1.3511.52050
X-RAY DIFFRACTIONr_mcangle_it2.18823284
X-RAY DIFFRACTIONr_scbond_it3.54531420
X-RAY DIFFRACTIONr_scangle_it5.54.51442
LS refinement shellResolution: 1.9→2.002 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.384 244
Rwork0.283 4257

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