[English] 日本語
Yorodumi
- PDB-3ie9: Structure of oxidized M98L mutant of amicyanin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ie9
TitleStructure of oxidized M98L mutant of amicyanin
ComponentsAmicyanin
KeywordsELECTRON TRANSPORT / TYPE-I BLUE COPPER PROTEIN / BETA SANDWICH / Copper / Metal-binding / Periplasm / 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
ACETATE ION / COPPER (II) ION / PHOSPHATE ION / Amicyanin
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSukumar, N. / Davidson, V.L.
CitationJournal: Biochemistry / Year: 2009
Title: Defining the role of the axial ligand of the type 1 copper site in amicyanin by replacement of methionine with leucine.
Authors: Choi, M. / Sukumar, N. / Liu, A. / Davidson, V.L.
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Structure summary
Category: audit_author / pdbx_unobs_or_zero_occ_atoms / software
Item: _audit_author.name
Revision 1.3Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_symmetry / _struct_conn_type.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 1.4Sep 6, 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: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8066
Polymers11,4871
Non-polymers3185
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Amicyanin
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)70,83336
Polymers68,9236
Non-polymers1,91130
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area8250 Å2
ΔGint-58 kcal/mol
Surface area25550 Å2
MethodPISA
3
A: Amicyanin
hetero molecules

A: Amicyanin
hetero molecules

A: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,41718
Polymers34,4613
Non-polymers95515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area1920 Å2
ΔGint-21 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.620, 99.620, 70.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-106-

PO4

21A-108-

ZN

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Amicyanin


Mass: 11487.133 Da / Num. of mol.: 1 / Fragment: residues 27-131 / Mutation: M98L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: ami, mauC / Plasmid: pMEG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22364

-
Non-polymers , 6 types, 87 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 4.39 Å3/Da / Density % sol: 71.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 3.2M Ammonium sulfate, 90mM Tris PH 8.0, 10mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.3808 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3808 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 12438 / % possible obs: 99 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 24.8
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.9 / % possible all: 96.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AAC

1aac


Resolution: 2.1→50 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 1.86 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.12 / Stereochemistry target values: ML
Details: PO4 CONTAINS TWO OXYGEN ATOMS INSTEAD OF FOUR. IT IS LOCATED ON A TWO-FOLD AXIS AND SYMMETRY GENERATES OTHER TWO OXYGEN ATOMS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1198 10.02 %random
Rwork0.185 ---
obs0.188 11953 95.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.218 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 72.19 Å2 / Biso mean: 37 Å2 / Biso min: 23.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.131 Å20 Å2-0 Å2
2--2.131 Å20 Å2
3----4.262 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 10 82 899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007836
X-RAY DIFFRACTIONf_angle_d1.0051130
X-RAY DIFFRACTIONf_chiral_restr0.07127
X-RAY DIFFRACTIONf_plane_restr0.006146
X-RAY DIFFRACTIONf_dihedral_angle_d15.952294

+
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