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- PDB-5lxz: W288A mutant of GlxA from Streptomyces lividans: Cu-bound form -

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Basic information

Entry
Database: PDB / ID: 5lxz
TitleW288A mutant of GlxA from Streptomyces lividans: Cu-bound form
ComponentsSecreted protein
KeywordsTRANSPORT PROTEIN / copper / metalloradical / AA5
Function / homology
Function and homology information


carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / GlxA beta barrel domain / Galactose oxidase-like, Early set domain / Galactose oxidase, central domain superfamily / Galactose oxidase-like, Early set domain / Kelch repeat type 2 / Kelch motif / Galactose oxidase/kelch, beta-propeller / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / PHOSPHATE ION / Secreted protein
Similarity search - Component
Biological speciesStreptomyces lividans TK24 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsChaplin, A.K. / Hough, M.A. / Worrall, J.A.R.
CitationJournal: to be published
Title: The role of a second-coordination sphere tryptophan residue in the maturation of the catalytic metalloradical site in the auxillary activity family 5 (AA5) GlxA from Streptomyces lividans
Authors: Chaplin, A.K. / Svistunenko, D.A. / Hough, M.A. / Wilson, M.T. / Vijgenboom, E. / Worrall, J.A.R.
History
DepositionSep 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: Secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,10417
Polymers66,0481
Non-polymers1,05616
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint5 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.510, 80.870, 140.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Secreted protein


Mass: 66048.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans TK24 (bacteria) / Gene: SLIV_23470 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6EWM0

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Non-polymers , 5 types, 681 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% PEG 20000, 0.1M sodium acetate pH 5 15 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2015
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→40.48 Å / Num. obs: 130534 / % possible obs: 99.5 % / Redundancy: 3.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.053 / Rrim(I) all: 0.106 / Net I/σ(I): 7.6 / Num. measured all: 480382 / Scaling rejects: 351
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2 / CC1/2: 0.616 / % possible all: 99.5

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4unm

4unm


Resolution: 1.49→40.48 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.117 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0578 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.058
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1812 6566 5 %RANDOM
Rwork0.1631 ---
obs0.164 123812 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.78 Å2 / Biso mean: 14.632 Å2 / Biso min: 5.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1.49→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 60 670 5367
Biso mean--28.47 25.9 -
Num. residues----601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194972
X-RAY DIFFRACTIONr_bond_other_d0.0080.024711
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.9756740
X-RAY DIFFRACTIONr_angle_other_deg1.012310886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55423.946223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11215827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1761536
X-RAY DIFFRACTIONr_chiral_restr0.1040.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215699
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021111
X-RAY DIFFRACTIONr_mcbond_it1.1271.2592485
X-RAY DIFFRACTIONr_mcbond_other1.1221.2572482
X-RAY DIFFRACTIONr_mcangle_it1.8121.8813120
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 462 -
Rwork0.271 9093 -
all-9555 -
obs--99.11 %

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