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- PDB-9gly: Structure of an ancestral laccase from Agaricales fungi -

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Basic information

Entry
Database: PDB / ID: 9gly
TitleStructure of an ancestral laccase from Agaricales fungi
ComponentsLaccase
KeywordsOXIDOREDUCTASE / Laccase / Ancestral
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsMedrano, F.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN) Spain
Citation
Journal: To Be Published
Title: Structure of an ancestral laccase
Authors: Medrano, F.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionAug 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,17812
Polymers53,1591
Non-polymers1,01911
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-38 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.660, 96.540, 57.058
Angle α, β, γ (deg.)90.000, 93.380, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-642-

HOH

21A-1003-

HOH

31A-1092-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Laccase


Mass: 53158.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Aspergillus oryzae (mold)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 555 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M TRIS-HCl at pH 7.0 containing 20% PEG 3000 and 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.54→48.27 Å / Num. obs: 67790 / % possible obs: 96.4 % / Redundancy: 7 % / Biso Wilson estimate: 16.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.151 / Rrim(I) all: 0.179 / Net I/σ(I): 9.7
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.759 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3302 / CC1/2: 0.55 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→48.27 Å / SU ML: 0.1762 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1869 1983 2.93 %
Rwork0.1677 65790 -
obs0.1683 67773 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.3 Å2
Refinement stepCycle: LAST / Resolution: 1.54→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 50 546 4358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673931
X-RAY DIFFRACTIONf_angle_d0.92125405
X-RAY DIFFRACTIONf_chiral_restr0.0603605
X-RAY DIFFRACTIONf_plane_restr0.0078721
X-RAY DIFFRACTIONf_dihedral_angle_d6.3721542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.30841370.27114622X-RAY DIFFRACTION94.99
1.58-1.620.26251370.2584613X-RAY DIFFRACTION95.27
1.62-1.670.35441420.25884666X-RAY DIFFRACTION95.53
1.67-1.730.26451370.23534683X-RAY DIFFRACTION95.86
1.73-1.790.25571410.20934632X-RAY DIFFRACTION96.17
1.79-1.860.22241440.1844687X-RAY DIFFRACTION96.29
1.86-1.940.1991330.17414708X-RAY DIFFRACTION96.61
1.94-2.050.19341460.17614742X-RAY DIFFRACTION96.96
2.05-2.170.19731500.16434704X-RAY DIFFRACTION97.27
2.17-2.340.2081250.16524410X-RAY DIFFRACTION89.98
2.34-2.580.20671500.16624776X-RAY DIFFRACTION98.01
2.58-2.950.20291400.16094820X-RAY DIFFRACTION98.22
2.95-3.720.15961460.14654828X-RAY DIFFRACTION98.79
3.72-48.270.12251550.13734899X-RAY DIFFRACTION98.94

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