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Basic information

Entry
Database: PDB / ID: 1rky
TitlePPLO + Xe
Componentslysyl oxidase
KeywordsOXIDOREDUCTASE / PPLO / lysyl oxidase / CAO / CuAO / copper-containing / amine oxidase / oxygen binding site / dioxygen binding site / xenon / TPQ / quinone / trihydroxyphenylalanine quinone
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor / diamine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding / plasma membrane
Similarity search - Function
Domain of unknown function DUF1965 / Domain of unknown function (DUF1965) / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, catalytic domain / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily ...Domain of unknown function DUF1965 / Domain of unknown function (DUF1965) / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, catalytic domain / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain / Beta-galactosidase; Chain A, domain 5 / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / IMIDAZOLE / XENON / : / Amine oxidase
Similarity search - Component
Biological speciesPichia pastoris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsGuss, J.M. / Duff, A.P.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Using Xenon as a Probe for Dioxygen-binding Sites in Copper Amine Oxidases
Authors: Duff, A.P. / Trambaiolo, D.M. / Cohen, A.E. / Ellis, P.J. / Juda, G.A. / Shepard, E.M. / Langley, D.B. / Dooley, D.M. / Freeman, H.C. / Guss, J.M.
History
DepositionNov 24, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_alt_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 / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_label_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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: lysyl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,30927
Polymers85,2891
Non-polymers3,02026
Water11,385632
1
A: lysyl oxidase
hetero molecules

A: lysyl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,61954
Polymers170,5782
Non-polymers6,04052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area26720 Å2
ΔGint-207 kcal/mol
Surface area50150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.144, 66.702, 108.620
Angle α, β, γ (deg.)90.00, 119.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-816-

CL

DetailsThe biological assembly is a dimer obtained by applying crystallographic symmetry to the monomer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein lysyl oxidase / PPLO


Mass: 85289.125 Da / Num. of mol.: 1 / Fragment: RESIDUES 41-787
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia pastoris (fungus) / Gene: ATCC 28, 485 / Plasmid: pPIC3 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115
References: GenBank: 13936870, UniProt: Q96X16*PLUS, protein-lysine 6-oxidase

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Sugars , 2 types, 5 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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.: 4
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 , 7 types, 653 molecules

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


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#9: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Xe
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 2.54 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 35% MPD, Imidazole pH 8.0, 200mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 300K. CRYSTAL EXPOSED TO XENON AT 300 PSI FOR 90 SECONDS THEN FROZEN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.552 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2003 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.552 Å / Relative weight: 1
ReflectionResolution: 1.68→31.46 Å / Num. obs: 99719 / % possible obs: 87.7 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.9
Reflection shellResolution: 1.68→1.74 Å / Mean I/σ(I) obs: 2.1 / % possible all: 84.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PPLO 1N9E chain A

1n9e


Resolution: 1.68→31.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.888 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REFMAC MATRIX WEIGHT = 0.3, BFACTOR WIEGHT = 0.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1705 1.9 %RANDOM
Rwork0.151 ---
obs0.151 85763 87.71 %-
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: 33.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.05 Å2
2--0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.68→31.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5933 0 120 632 6685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216388
X-RAY DIFFRACTIONr_bond_other_d0.0020.025336
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9558727
X-RAY DIFFRACTIONr_angle_other_deg0.834312479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7825741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027106
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021320
X-RAY DIFFRACTIONr_nbd_refined0.1920.21054
X-RAY DIFFRACTIONr_nbd_other0.250.26106
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.23615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2481
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.213
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.2217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it4.88923721
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.50136072
X-RAY DIFFRACTIONr_scbond_it8.04222662
X-RAY DIFFRACTIONr_scangle_it10.41632645
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free21.58621
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 108
Rwork0.292 6124

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