[English] 日本語
Yorodumi
- PDB-1aiz: STRUCTURE OF APO-AZURIN FROM ALCALIGENES DENITRIFICANS AT 1.8 ANG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1aiz
TitleSTRUCTURE OF APO-AZURIN FROM ALCALIGENES DENITRIFICANS AT 1.8 ANGSTROMS RESOLUTION
ComponentsAZURIN
KeywordsELECTRON TRANSPORT(CADMIUM BINDING)
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Azurin / : / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesAchromobacter denitrificans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBaker, E.N. / Anderson, B.F. / Blackwell, K.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure of apo-azurin from Alcaligenes denitrificans at 1.8 A resolution.
Authors: Shepard, W.E. / Kingston, R.L. / Anderson, B.F. / Baker, E.N.
#1: Journal: J.Am.Chem.Soc. / Year: 1990
Title: Copper Coordination Geometry in Azurin Undergoes Minimal Change on Reduction of Copper(II) to Copper(I)
Authors: Shepard, W.E.B. / Anderson, B.F. / Lewandoski, D.A. / Norris, G.E. / Baker, E.N.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Structure of Azurin from Alcaligenes Denitrificans: Refinement at 1.8 Angstroms Resolution and Comparison of the Two Crystallographically Independent Molecules
Authors: Baker, E.N.
History
DepositionNov 11, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AZURIN
B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6258
Polymers28,0162
Non-polymers6096
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-51 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.150, 74.350, 99.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.101, 0.9948, 0.0166), (0.9944, 0.1004, 0.0336), (0.0318, 0.0199, -0.9993)
Vector: 0.7969, -1.016, 24.391)

-
Components

#1: Protein AZURIN


Mass: 14008.003 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter denitrificans (bacteria) / References: UniProt: P00280
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal grow
*PLUS
pH: 6 / Method: interface diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mphosphate11
240 %satammonium sulphate11
314 mg/mlprotein11
480 %satammonium sulfate12

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.168 23349
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 22 239 2215
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.015
X-RAY DIFFRACTIONp_angle_d0.0460.046
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.049
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it4.24.2
X-RAY DIFFRACTIONp_mcangle_it6.16.1
X-RAY DIFFRACTIONp_scbond_it6.16.1
X-RAY DIFFRACTIONp_scangle_it9.39.3
X-RAY DIFFRACTIONp_plane_restr0.0130.013
X-RAY DIFFRACTIONp_chiral_restr0.1880.188
X-RAY DIFFRACTIONp_singtor_nbd0.1860.186
X-RAY DIFFRACTIONp_multtor_nbd0.2330.233
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1910.191
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.52.5
X-RAY DIFFRACTIONp_staggered_tor18.718.7
X-RAY DIFFRACTIONp_orthonormal_tor29.329.3
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

+
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