2Q5B | pdb_00002q5b

High resolution structure of Plastocyanin from Phormidium laminosum

PDB DOI: https://doi.org/10.2210/pdb2Q5B/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Leptolyngbya laminosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-05-31 Released: 2008-06-17
Deposition Author(s): Fromme, R., Bukhman-DeRuyter, Y.S., Grotjohann, I., Mi, H., Fromme, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Plastocyanin at high resolution from Phormidium laminosum and the double mutant D44A, D45A

Bukhman-DeRuyter, Y.S., Fromme, R., Grotjohann, I., Schlarb-Ridley, B., Mi, H., Fromme, P.

To be published.

Macromolecule Content

Total Structure Weight: 35 kDa
Atom Count: 2,716
Modeled Residue Count: 315
Deposited Residue Count: 315
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plastocyanin	A, B, C	105	N/A	Mutation(s): 0 Gene Names: petE
UniProt
Find proteins for Q51883 (Leptolyngbya laminosa) Explore Q51883 Go to UniProtKB: Q51883
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q51883
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], M [auth C], N [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B], L [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain L [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], K [auth B], O [auth C], P [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.210 (Depositor), 0.210 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.329	α = 90
b = 84.329	β = 90
c = 90.536	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-06-17

Deposition Author(s):

Fromme, R.

Bukhman-DeRuyter, Y.S.

Grotjohann, I.

Mi, H.

Fromme, P.

Revision History (Full details and data files)

Version 1.0: 2008-06-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description