[English] 日本語
Yorodumi
- PDB-2q5b: High resolution structure of Plastocyanin from Phormidium laminosum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q5b
TitleHigh resolution structure of Plastocyanin from Phormidium laminosum
ComponentsPlastocyanin
KeywordsELECTRON TRANSPORT / Plastocyanin / Photosystem 1
Function / homology
Function and homology information


plasma membrane-derived thylakoid membrane / electron transfer activity / copper ion binding
Similarity search - Function
Plastocyanin, cyanobacteria / Plastocyanin / 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 ...Plastocyanin, cyanobacteria / Plastocyanin / 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 / : / Plastocyanin
Similarity search - Component
Biological speciesPhormidium laminosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsFromme, R. / Bukhman-DeRuyter, Y.S. / Grotjohann, I. / Mi, H. / Fromme, P.
CitationJournal: To be Published
Title: Plastocyanin at high resolution from Phormidium laminosum and the double mutant D44A, D45A
Authors: Bukhman-DeRuyter, Y.S. / Fromme, R. / Grotjohann, I. / Schlarb-Ridley, B. / Mi, H. / Fromme, P.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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 / _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: Plastocyanin
B: Plastocyanin
C: Plastocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,00216
Polymers34,2953
Non-polymers70713
Water4,828268
1
A: Plastocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6986
Polymers11,4321
Non-polymers2665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Plastocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6004
Polymers11,4321
Non-polymers1683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
3
C: Plastocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7046
Polymers11,4321
Non-polymers2735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-128 kcal/mol
Surface area14040 Å2
MethodPISA
5
C: Plastocyanin
hetero molecules

A: Plastocyanin
hetero molecules

B: Plastocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,00216
Polymers34,2953
Non-polymers70713
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y+1/2,-z-1/41
crystal symmetry operation8_564-y,-x+1,-z-1/21
Buried area2530 Å2
ΔGint-108 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.329, 84.329, 90.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-534-

HOH

DetailsThe biological unit is the monomer.

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Plastocyanin


Mass: 11431.800 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phormidium laminosum (bacteria) / Gene: petE / Plasmid: pET11Pc / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q51883

-
Non-polymers , 5 types, 281 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.34 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M NA CACODYLATE BUFFER (PH 6), 0.2 M ZN ACETATE, 15% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→42.11 Å / Num. all: 57906 / Num. obs: 57906 / % possible obs: 99.6 % / Redundancy: 9.6 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.4
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2 / % possible all: 96

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASER1.3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BAW

1baw


Resolution: 1.45→9.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.541 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.07
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21017 2920 5.1 %RANDOM
Rwork0.18972 ---
obs0.19075 54607 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.719 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.45→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 16 268 2699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222501
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9583402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.23125.143105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50215391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.742153
X-RAY DIFFRACTIONr_chiral_restr0.0850.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021931
X-RAY DIFFRACTIONr_nbd_refined0.2620.21157
X-RAY DIFFRACTIONr_nbtor_refined0.310.21656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2241
X-RAY DIFFRACTIONr_metal_ion_refined0.060.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7750.232
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0440.21
X-RAY DIFFRACTIONr_mcbond_it0.8671.51575
X-RAY DIFFRACTIONr_mcangle_it1.48622548
X-RAY DIFFRACTIONr_scbond_it2.2073938
X-RAY DIFFRACTIONr_scangle_it3.1244.5853
X-RAY DIFFRACTIONr_rigid_bond_restr1.72332513
X-RAY DIFFRACTIONr_sphericity_free2.7393302
X-RAY DIFFRACTIONr_sphericity_bonded2.13832432
LS refinement shellResolution: 1.452→1.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 190 -
Rwork0.279 3615 -
obs--92.29 %

+
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