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- PDB-5ez7: Crystal structure of the FAD dependent oxidoreductase PA4991 from... -

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Basic information

Entry
Database: PDB / ID: 5ez7
TitleCrystal structure of the FAD dependent oxidoreductase PA4991 from Pseudomonas aeruginosa
Componentsflavoenzyme PA4991
KeywordsOXIDOREDUCTASE / flavoenzyme / flavine
Function / homology
Function and homology information


Oxidoreductases / FAD binding / oxidoreductase activity / cytoplasm
Similarity search - Function
FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / Probable FAD-dependent oxidoreductase PA4991
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJacewicz, A. / Schnell, R. / Lindqvist, Y. / Schneider, G.
Funding support Sweden, 2items
OrganizationGrant numberCountry
European Commission Sweden
Swedish Research Council Sweden
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of the flavoenzyme PA4991 from Pseudomonas aeruginosa.
Authors: Jacewicz, A. / Schnell, R. / Lindqvist, Y. / Schneider, G.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: flavoenzyme PA4991
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4384
Polymers42,2511
Non-polymers1,1873
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-66 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.890, 79.830, 63.230
Angle α, β, γ (deg.)90.00, 104.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein flavoenzyme PA4991


Mass: 42251.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA4991 / Plasmid: pNIC28Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HUH4
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M trimethylamine N-oxide, 20% PEG2000 monomethyl-ether, 0.1 M Tris-HCl pH 8.5
PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0093 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 2.4→61.32 Å / Num. obs: 14372 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 41.2 Å2 / Rsym value: 0.072 / Net I/σ(I): 17.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 5.3 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ab initio model from Rosetta

Resolution: 2.4→48.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.339 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.486 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22838 718 5 %RANDOM
Rwork0.17344 ---
obs0.17611 13625 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.865 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å21.57 Å2
2--1.05 Å2-0 Å2
3----1.12 Å2
Refinement stepCycle: 1 / Resolution: 2.4→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2766 0 55 41 2862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192877
X-RAY DIFFRACTIONr_bond_other_d0.0020.022801
X-RAY DIFFRACTIONr_angle_refined_deg1.7172.0073912
X-RAY DIFFRACTIONr_angle_other_deg0.98936420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3675360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.76122.52123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2915467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2081534
X-RAY DIFFRACTIONr_chiral_restr0.0940.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213229
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02634
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.462.7061449
X-RAY DIFFRACTIONr_mcbond_other1.462.7041448
X-RAY DIFFRACTIONr_mcangle_it2.5614.0441806
X-RAY DIFFRACTIONr_mcangle_other2.5614.0451807
X-RAY DIFFRACTIONr_scbond_it1.5782.891428
X-RAY DIFFRACTIONr_scbond_other1.5772.8891429
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7284.2412107
X-RAY DIFFRACTIONr_long_range_B_refined4.44521.3393067
X-RAY DIFFRACTIONr_long_range_B_other4.4421.3323062
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 52 -
Rwork0.225 962 -
obs--97.13 %
Refinement TLS params.Method: refined / Origin x: 34.729 Å / Origin y: -4.516 Å / Origin z: 8.848 Å
111213212223313233
T0.0435 Å20.0215 Å2-0.0056 Å2-0.0338 Å2-0.0066 Å2--0.0051 Å2
L1.1121 °20.1272 °2-0.6399 °2-0.7109 °20.0816 °2--3.7925 °2
S0.0183 Å °0.0128 Å °0.0373 Å °-0.0587 Å °0.0198 Å °0.033 Å °-0.2541 Å °-0.114 Å °-0.038 Å °

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