[English] 日本語
Yorodumi
- PDB-1pf3: Crystal Structure of the M441L mutant of the multicopper oxidase CueO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pf3
TitleCrystal Structure of the M441L mutant of the multicopper oxidase CueO
ComponentsBlue copper oxidase cueO
KeywordsOXIDOREDUCTASE / copper / multicopper oxidase
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / oxidoreductase activity, acting on metal ions / detoxification of copper ion / response to copper ion / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / ferroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CU-CL-CU LINKAGE / COPPER (II) ION / Multicopper oxidase CueO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsRoberts, S.A. / Wildner, G.F. / Grass, G. / Weichsel, A. / Ambrus, A. / Rensing, C. / Montfort, W.R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: A Labile Regulatory Copper Ion Lies Near the T1 Copper Site in the Multicopper Oxidase CueO.
Authors: Roberts, S.A. / Wildner, G.F. / Grass, G. / Weichsel, A. / Ambrus, A. / Rensing, C. / Montfort, W.R.
History
DepositionMay 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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.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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Blue copper oxidase cueO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9414
Polymers54,6521
Non-polymers2903
Water7,692427
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.445, 91.193, 53.905
Angle α, β, γ (deg.)90.00, 102.35, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Blue copper oxidase cueO / Copper efflux oxidase


Mass: 54651.520 Da / Num. of mol.: 1 / Mutation: M441L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CUEO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P36649
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-C2C / CU-CL-CU LINKAGE


Mass: 162.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: ClCu2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% PEG, 200 mM ammonium acetate, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 22K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. all: 63714 / Num. obs: 63714 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rsym value: 0.066 / Net I/σ(I): 20.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 7119 / Rsym value: 0.18 / % possible all: 94

-
Processing

Software
NameVersionClassification
REFMAC5.1.22refinement
CrystalClearD*TREK (MSC/RIGAKU)data scaling
RefinementStarting model: pdb entry 1KV7

1kv7


Resolution: 1.5→10 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.227 / SU ML: 0.048
Isotropic thermal model: Isotropic, except copper, chlorine anisotropic
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The T1 copper is partially depleted (around 50% occupancy) The T2 copper is somewhat less depleted. MISSING FROM THE MODEL ARE RESIDUES 1- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The T1 copper is partially depleted (around 50% occupancy) The T2 copper is somewhat less depleted. MISSING FROM THE MODEL ARE RESIDUES 1-30 AT THE N-TERMINUS (1-28 ARE A PRESUMABLY CLEAVED SIGNAL PEPTIDE, 29-30 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP), AND RESIDUES 380-402 WHICH ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP AND, PRESUMABLY, DISORDERED. A strep tag on the C terminus has not been cleaved but is not visible in the electron density maps.
RfactorNum. reflection% reflectionSelection details
Rfree0.22757 3211 5 %from pdb entry 1KV7
Rwork0.19099 ---
obs0.19283 63714 83.74 %-
all-63714 --
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: 15.712 Å2
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 5 427 3997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213657
X-RAY DIFFRACTIONr_bond_other_d0.0020.023335
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9564970
X-RAY DIFFRACTIONr_angle_other_deg0.85137784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6785463
X-RAY DIFFRACTIONr_chiral_restr0.0970.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024073
X-RAY DIFFRACTIONr_gen_planes_other0.010.02680
X-RAY DIFFRACTIONr_nbd_refined0.2040.2589
X-RAY DIFFRACTIONr_nbd_other0.2540.23794
X-RAY DIFFRACTIONr_nbtor_other0.0850.22144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.29
X-RAY DIFFRACTIONr_mcbond_it0.9271.52308
X-RAY DIFFRACTIONr_mcangle_it1.62523721
X-RAY DIFFRACTIONr_scbond_it2.59231349
X-RAY DIFFRACTIONr_scangle_it4.0914.51249
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.206 284
Rwork0.184 5148

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more