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- PDB-1n9e: Crystal structure of Pichia pastoris Lysyl Oxidase PPLO -

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Basic information

Entry
Database: PDB / ID: 1n9e
TitleCrystal structure of Pichia pastoris Lysyl Oxidase PPLO
ComponentsLYSYL OXIDASE
KeywordsOXIDOREDUCTASE / AMINE OXIDASE / QUINOPROTEIN / TOPAQUINONE ENZYME / TPQ
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor / diamine oxidase activity / primary amine 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 / : / Amine oxidase
Similarity search - Component
Biological speciesPichia pastoris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGuss, J.M. / Duff, A.P.
CitationJournal: Biochemistry / Year: 2003
Title: The Crystal Structure of Pichia pastoris Lysyl Oxidase
Authors: Duff, A.P. / Cohen, A.E. / Ellis, P.J. / Kuchar, J.A. / Langley, D.B. / Shepard, E.M. / Dooley, D.M. / Freeman, H.C. / Guss, J.M.
History
DepositionNov 24, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 29, 2014Group: Derived calculations
Revision 1.4Feb 7, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _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 / _struct_conn.ptnr2_label_seq_id
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 / pdbx_unobs_or_zero_occ_residues
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
B: LYSYL OXIDASE
C: LYSYL OXIDASE
D: LYSYL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,70464
Polymers359,2034
Non-polymers8,50260
Water71,7183981
1
A: LYSYL OXIDASE
B: LYSYL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,85232
Polymers179,6012
Non-polymers4,25130
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24140 Å2
ΔGint-308 kcal/mol
Surface area49490 Å2
MethodPISA
2
C: LYSYL OXIDASE
D: LYSYL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,85232
Polymers179,6012
Non-polymers4,25130
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24050 Å2
ΔGint-309 kcal/mol
Surface area49630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)248.442, 121.125, 151.841
Angle α, β, γ (deg.)90.00, 124.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
LYSYL OXIDASE /


Mass: 89800.625 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pichia pastoris (fungus)
References: GenBank: 13936870, UniProt: Q96X16*PLUS, protein-lysine 6-oxidase

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Sugars , 2 types, 20 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.: 4
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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16
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 , 4 types, 4021 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3981 / 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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 25% PEG 4000, 0.175M ammonium sulfate, 15% MPD, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Lee, M., (2002) Acta Cryst., D58, 2177.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
225 %PEG40001reservoir
3175 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.99184
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 17, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99184 Å / Relative weight: 1
ReflectionResolution: 1.65→24.6 Å / Num. obs: 419014 / % possible obs: 94.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.1
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.2
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 24.6 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Lowest resolution: 1.68 Å / % possible obs: 90.7 % / Redundancy: 2.6 % / Num. unique obs: 28231 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OAC

1oac


Resolution: 1.65→24.6 Å / Cor.coef. Fo:Fc: 0.964 / SU B: 1.493 / SU ML: 0.05 / Cross valid method: THROUGHOUT, EXCEPT FINAL ROUND / ESU R: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE STRUCTURE WAS ALSO REFINED WITH CNS VER.1.1 SO4 811, 821, 831 AND 841 ARE MODELLED WITH ZERO OCCUPANCY. ELECTRON DENSITY FOR THESE IONS STRONGLY SUGGESTS THEIR PRESENCE, HOWEVER, THE ...Details: THE STRUCTURE WAS ALSO REFINED WITH CNS VER.1.1 SO4 811, 821, 831 AND 841 ARE MODELLED WITH ZERO OCCUPANCY. ELECTRON DENSITY FOR THESE IONS STRONGLY SUGGESTS THEIR PRESENCE, HOWEVER, THE MODELLED POSITIONS ARE NOT STABLE IN POSITIONAL REFINEMENT, AND RESULTING REFINED POSITIONS HAVE UNACCEPTABLE VAN DER WAALS VIOLATIONS WITH NEIGHBOURING PROTEIN ATOMS. FREE_R WAS MONITORED IN ALL ROUNDS OF REFINEMENT EXCEPT THE LAST. THE TEST SET SIZE WAS 5%, AND WAS SELECTED RANDOMLY. IN THE LAST ROUND OF REFINEMENT, THE MODEL WAS REFINED AGAINST ALL OF THE DATA TO PRODUCE THE FINAL MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.18673 20998 5 %RANDOM
Rwork0.1605 ---
all0.16029 ---
obs0.16029 419014 94.7 %-
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: 17.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20.58 Å2
2--0.21 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.65→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23704 0 488 3981 28173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02124919
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.95434019
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58932952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4154024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.23604
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0219536
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3460.311694
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.54305
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.361
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.547
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.6044.514700
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.52623806
X-RAY DIFFRACTIONr_scbond_it3.852910219
X-RAY DIFFRACTIONr_scangle_it5.98313.510201
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 1518
Rwork0.234 28231
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 24.6 Å / % reflection Rfree: 5 % / Rfactor all: 0.16 / Rfactor Rfree: 0.187 / Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5
LS refinement shell
*PLUS
Lowest resolution: 1.68 Å / Rfactor Rwork: 0.24 / Rfactor obs: 0.23

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