[English] 日本語
Yorodumi
- PDB-5vde: Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vde
TitleCrystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form I
ComponentsMetal homeostasis factor ATX1
KeywordsMETAL BINDING PROTEIN / Atx1 / metallochaperone / copper transfer / metal-binding domain / ferredoxin-like fold
Function / homology
Function and homology information


copper chaperone activity / copper ion transport / cellular response to oxidative stress / intracellular iron ion homeostasis / metal ion binding / cytosol
Similarity search - Function
: / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (I) ION / Copper chaperone ATX1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLee, M. / Maher, M.J.
CitationJournal: J. Inorg. Biochem. / Year: 2017
Title: The crystal structures of a copper-bound metallochaperone from Saccharomyces cerevisiae.
Authors: Lee, M. / Cooray, N.D.G. / Maher, M.J.
History
DepositionApr 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metal homeostasis factor ATX1
B: Metal homeostasis factor ATX1
C: Metal homeostasis factor ATX1
D: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0586
Polymers32,9314
Non-polymers1272
Water4,107228
1
A: Metal homeostasis factor ATX1
B: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5293
Polymers16,4652
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Metal homeostasis factor ATX1
D: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5293
Polymers16,4652
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Metal homeostasis factor ATX1
B: Metal homeostasis factor ATX1
hetero molecules

C: Metal homeostasis factor ATX1
D: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0586
Polymers32,9314
Non-polymers1272
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area2940 Å2
ΔGint-35 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.976, 80.054, 50.763
Angle α, β, γ (deg.)90.00, 99.91, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Metal homeostasis factor ATX1


Mass: 8232.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ATX1, YNL259C, N0840 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38636
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1 M HEPES (pH 7.3), 24% (W/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 34104 / % possible obs: 97.3 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.057 / Net I/σ(I): 10.2
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 4.7 % / Num. unique obs: 2129 / CC1/2: 0.748 / Rpim(I) all: 0.499 / % possible all: 89

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CC8

1cc8


Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.121 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.20589 1710 5.2 %RANDOM
Rwork0.16372 ---
obs0.16593 31480 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.974 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å2-1.44 Å2
2--0.28 Å20 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 2 228 2474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022336
X-RAY DIFFRACTIONr_bond_other_d0.0020.022337
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9953154
X-RAY DIFFRACTIONr_angle_other_deg1.02635484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.13126.27986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19315492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.744154
X-RAY DIFFRACTIONr_chiral_restr0.1250.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02395
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9041.6181154
X-RAY DIFFRACTIONr_mcbond_other1.8521.6141153
X-RAY DIFFRACTIONr_mcangle_it2.7372.4061441
X-RAY DIFFRACTIONr_mcangle_other2.7562.411442
X-RAY DIFFRACTIONr_scbond_it3.3452.1121182
X-RAY DIFFRACTIONr_scbond_other3.3382.1121182
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2462.9711702
X-RAY DIFFRACTIONr_long_range_B_refined6.88120.9612607
X-RAY DIFFRACTIONr_long_range_B_other6.79820.4592560
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 127 -
Rwork0.245 2129 -
obs--89.03 %

+
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