[English] 日本語
Yorodumi
- PDB-1bxa: AMICYANIN REDUCED, PH 4.4, 1.3 ANGSTROMS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bxa
TitleAMICYANIN REDUCED, PH 4.4, 1.3 ANGSTROMS
ComponentsPROTEIN (AMICYANIN)
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Amicyanin, Paracoccus/Methylobacterium / Amicyanin / : / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 ...Amicyanin, Paracoccus/Methylobacterium / Amicyanin / : / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / 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 (I) ION / Amicyanin
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.3 Å
AuthorsCunane, L.M. / Chen, Z.W. / Durley, R.C.E. / Mathews, F.S.
Citation
Journal: Biochemistry / Year: 1998
Title: Molecular basis for interprotein complex-dependent effects on the redox properties of amicyanin.
Authors: Zhu, Z. / Cunane, L.M. / Chen, Z. / Durley, R.C. / Mathews, F.S. / Davidson, V.L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: X-Ray Structure of the Cupredoxin Amicyanin, from Paracoccus Denitrificans, Refined at 1.31 A Resolution
Authors: Cunane, L.M. / Chen, Z.-W. / Durley, R.C.E. / Mathews, F.S.
History
DepositionOct 1, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 7, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (AMICYANIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5692
Polymers11,5051
Non-polymers641
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.960, 56.910, 27.610
Angle α, β, γ (deg.)90.00, 96.81, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PROTEIN (AMICYANIN)


Mass: 11505.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / Strain: NCIB 8944 / References: UniProt: P22364
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.96 Å3/Da / Density % sol: 32 %
Crystal growpH: 4.38 / Details: pH 4.38
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 Mphosphate1reservoir
290 %sodium monobasic1reservoir
310 %potassium dibasic1reservoir
4protein1drop

-
Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.3→19.8 Å / Num. obs: 21062 / % possible obs: 95 % / Redundancy: 4.9 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 18
Reflection shellResolution: 1.3→1.45 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 4 / % possible all: 84
Reflection
*PLUS
Redundancy: 4.9 %
Reflection shell
*PLUS
% possible obs: 71 % / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.8

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
UCSD-systemdata reduction
UCSD-systemdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: 1AAC

1aac


Resolution: 1.3→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2019 9.9 %RANDOM
Rwork0.169 ---
obs0.169 20292 93.6 %-
Displacement parametersBiso mean: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 1 104 912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.911.5
X-RAY DIFFRACTIONx_mcangle_it1.492
X-RAY DIFFRACTIONx_scbond_it1.842
X-RAY DIFFRACTIONx_scangle_it3.022.5
LS refinement shellResolution: 1.3→1.38 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 257 10.6 %
Rwork0.227 2179 -
obs--67.6 %
Xplor fileSerial no: 1 / Param file: AMIRED4.PAR / Topol file: AMIRED4.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.55

+
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