4LYC | pdb_00004lyc

Cd ions within a lysoyzme single crystal

PDB DOI: https://doi.org/10.2210/pdb4LYC/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2013-07-30 Released: 2015-02-25
Deposition Author(s): Wei, H., House, S., Wu, J., Zhang, J., Wang, Z., He, Y., Gao, Y.-G., Robinson, H., Li, W., Zuo, J.-M., Robertson, I.M., Lu, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.250 (DCC)
R-Value Work:
0.228 (Depositor), 0.225 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Enhanced and tunable fluorescent quantum dots within a single crystal of protein

Wei, H., House, S., Wu, J., Zhang, J., Wang, Z., He, Y., Gao, Y.-G., Robinson, H., Li, W., Zuo, J.-M., Robertson, I.M., Lu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 15.34 kDa
Atom Count: 1,160
Modelled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0 Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth A] SDF format, chain B [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain C [auth A] MOL2 format, chain J [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain C [auth A] mmCIF format, chain J [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.250 (DCC)
R-Value Work: 0.228 (Depositor), 0.225 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.558	α = 90
b = 78.558	β = 90
c = 37.179	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
SHELX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-02-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-02-25
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary