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- PDB-3qpk: Probing oxygen channels in Melanocarpus albomyces laccase -

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Basic information

Entry
Database: PDB / ID: 3qpk
TitleProbing oxygen channels in Melanocarpus albomyces laccase
ComponentsLaccase-1
KeywordsOXIDOREDUCTASE / Cu Binding / Xe binding / laccase / multicopper oxidase
Function / homology
Function and homology information


extraorganismal space / lignin catabolic process / hydroquinone:oxygen oxidoreductase activity / laccase / cellulose catabolic process / copper ion binding
Similarity search - Function
Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal ...Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / XENON / Laccase-1
Similarity search - Component
Biological speciesMelanocarpus albomyces (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKallio, J.P. / Rouvinen, J. / Hakulinen, N.
CitationJournal: Biochemistry / Year: 2011
Title: Probing the Dioxygen Route in Melanocarpus albomyces Laccase with Pressurized Xenon Gas.
Authors: Kallio, J.P. / Rouvinen, J. / Kruus, K. / Hakulinen, N.
History
DepositionFeb 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Laccase-1
B: Laccase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,32732
Polymers123,6912
Non-polymers5,63630
Water22,0501224
1
A: Laccase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,86117
Polymers61,8451
Non-polymers3,01616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Laccase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,46615
Polymers61,8451
Non-polymers2,62014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.150, 60.200, 114.440
Angle α, β, γ (deg.)90.00, 99.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Laccase-1 / Benzenediol:oxygen oxidoreductase 1 / Diphenol oxidase 1 / Ligninolytic phenoloxidase / Urishiol oxidase 1


Mass: 61845.441 Da / Num. of mol.: 2 / Fragment: mature enzyme (UNP residues 51-609)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melanocarpus albomyces (fungus) / Gene: LAC1 / Production host: Hypocrea jecorina (fungus) / References: UniProt: Q70KY3, laccase

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Sugars , 2 types, 12 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 5
Source method: isolated from a genetically manipulated source
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, 1242 molecules

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


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Xe
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1224 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 13% w/v P2000 MME, 0.2 M ammonium sulfate, 0.05 M magnesium sulfate, 0.1 M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2010 / Details: Si(311) monochromator
RadiationMonochromator: Si(311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→43.825 Å / Num. all: 92416 / Num. obs: 91675 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.9679 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.199 / % possible all: 99.3

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XDSSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q90

2q90
PDB Unreleased entry


Resolution: 1.9→43.825 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 27.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 4584 5 %RANDOM
Rwork0.2145 ---
obs0.2173 91675 99.23 %-
all-91675 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.52 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.3903 Å2-0 Å2-0.3689 Å2
2---4.5098 Å2-0 Å2
3---9.9001 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8738 0 292 1224 10254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0229342
X-RAY DIFFRACTIONf_angle_d1.1112843
X-RAY DIFFRACTIONf_dihedral_angle_d16.8393288
X-RAY DIFFRACTIONf_chiral_restr0.0721418
X-RAY DIFFRACTIONf_plane_restr0.0051675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.30564540.22388628X-RAY DIFFRACTION99
1.9679-2.04670.30854580.21658700X-RAY DIFFRACTION99
2.0467-2.13990.29264570.20868695X-RAY DIFFRACTION99
2.1399-2.25270.30154570.21588666X-RAY DIFFRACTION99
2.2527-2.39380.30384560.22038673X-RAY DIFFRACTION99
2.3938-2.57860.26674570.2088680X-RAY DIFFRACTION99
2.5786-2.83810.27314570.21628687X-RAY DIFFRACTION99
2.8381-3.24860.26464590.21088723X-RAY DIFFRACTION99
3.2486-4.09240.23274620.19848775X-RAY DIFFRACTION99
4.0924-43.8370.2474670.22428864X-RAY DIFFRACTION98

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