[English] 日本語
Yorodumi
- PDB-2aza: STRUCTURE OF AZURIN FROM ALCALIGENES DENITRIFICANS. REFINEMENT AT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2aza
TitleSTRUCTURE OF AZURIN FROM ALCALIGENES DENITRIFICANS. REFINEMENT AT 1.8 ANGSTROMS RESOLUTION AND COMPARISON OF THE TWO CRYSTALLOGRAPHICALLY INDEPENDENT MOLECULES
ComponentsAZURIN
KeywordsELECTRON TRANSPORT PROTEIN(CUPROPROTEIN)
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
COPPER (II) ION / Azurin
Similarity search - Component
Biological speciesAchromobacter xylosoxidans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBaker, E.N. / Norris, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1988
Title: Structure of azurin from Alcaligenes denitrificans refinement at 1.8 A resolution and comparison of the two crystallographically independent molecules.
Authors: Baker, E.N.
#1: Journal: J.Am.Chem.Soc. / Year: 1986
Title: Blue Copper Proteins. The Copper Site in Azurin from Alcaligenes Denitrificans
Authors: Norris, G.E. / Anderson, B.F. / Baker, E.N.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Azurin from Alcaligenes Denitrificans at 2.5 Angstroms Resolution
Authors: Norris, G.E. / Anderson, B.F. / Baker, E.N.
#3: Journal: J.Mol.Biol. / Year: 1979
Title: Purification and Preliminary Crystallographic Studies on Azurin and Cytochrome C(Prime) from Alcaligenes Denitrificans and Alcaligenes Sp. Ncib 11015
Authors: Norris, G.E. / Anderson, B.F. / Baker, E.N. / Rumball, S.V.
#4: Journal: Recent Developments in the Chemical Study of Protein Structures
Year: 1971
Authors: Ambler, R.P.
History
DepositionOct 14, 1986Processing site: BNL
SupersessionJan 15, 1987ID: 1AZA
Revision 1.0Jan 15, 1987Provider: 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
Remark 700SHEET STRAND 1 OF SHEET B1A (AND B1B) AND STRAND 1 OF SHEET B2A (AND B2B) ARE PARTS OF A PIECE OF ...SHEET STRAND 1 OF SHEET B1A (AND B1B) AND STRAND 1 OF SHEET B2A (AND B2B) ARE PARTS OF A PIECE OF EXTENDED CHAIN WHICH IS SPLIT BETWEEN BETWEEN THE TWO SHEETS. RESIDUES 14-16 BELONG TO SHEET B1 AND RESIDUES 18-22 BELONG TO SHEET B2 WITH A KINK IN BETWEEN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AZURIN
B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4117
Polymers27,9962
Non-polymers4155
Water5,062281
1
A: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2544
Polymers13,9981
Non-polymers2563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AZURIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1583
Polymers13,9981
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.000, 74.200, 99.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: SEE REMARK 5. / 2: SEE REMARK 6. / 3: SEE REMARKS 5 AND 6.
Components on special symmetry positions
IDModelComponents
11A-136-

SO4

21A-240-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.10158, 0.99439, 0.02952), (0.99461, 0.1009, 0.02393), (0.02081, 0.03179, -0.99928)
Vector: 0.79, -1.085, 24.503)
DetailsTHE TRANSFORMATION PROVIDED ON THE *MTRIX* RECORDS BELOW WILL PRODUCE APPROXIMATE COORDINATES FOR MOLECULE 1 (CHAIN INDICATOR *A*) WHEN APPLIED TO THE COORDINATES OF MOLECULE 2 (CHAIN INDICATOR *B*).

-
Components

#1: Protein AZURIN


Mass: 13997.919 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter xylosoxidans (bacteria) / References: UniProt: P00280
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTURNS 3A AND 12A (AND 3B AND 12B) ARE MORE LIKE ALPHA-TURNS AS THEY HAVE GOOD 1-5 H-BONDS (O ALA 40 ...TURNS 3A AND 12A (AND 3B AND 12B) ARE MORE LIKE ALPHA-TURNS AS THEY HAVE GOOD 1-5 H-BONDS (O ALA 40 - N MET 44 AND O HIS 117 - N MET 121) WHICH ARE SHORTER THAN THE 1-4 H-BONDS (O ALA 40 - MET 43 AND 0 HIS 117 - N MET 120).
Sequence detailsRESIDUE 42 IS INCLUDED HERE AS SER BOTH IN THE *ATOM* AND *SEQRES* RECORDS. RESIDUE 42 IS ALA IN ...RESIDUE 42 IS INCLUDED HERE AS SER BOTH IN THE *ATOM* AND *SEQRES* RECORDS. RESIDUE 42 IS ALA IN THE CHEMICALLY DETERMINED SEQUENCE. RESIDUE 43 IS INCLUDED HERE AS ALA IN BOTH THE *ATOM* AND *SEQRES* RECORDS. RESIDUE 43 IS VAL IN THE CHEMICALLY DETERMINED SEQUENCE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal grow
*PLUS
pH: 5 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mphosphate11
275 %satammonium sulphate11

-
Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 21980 / % possible obs: 87 %

-
Processing

SoftwareName: TNT / Classification: refinement
RefinementHighest resolution: 1.8 Å
Details: ONLY INTERNAL H-BONDS INVOLVING SIDE CHAINS OR CROSSLINKING H BONDS BETWEEN STRANDS ARE PRESENTED ON THE CONECT RECORDS BELOW.
RfactorNum. reflection
obs0.157 21980
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 13 281 2263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.9
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rfactor all: 0.157 / Num. reflection all: 21980
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

+
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://pdbjlvh1.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