5M1Y | pdb_00005m1y

The case of 1lkr held at the PDB and its variable amino acid occupancies; re refinement of 4ow9 to correct this

PDB DOI: https://doi.org/10.2210/pdb5M1Y/pdb
Entry: 5M1Y supersedes: 4OW9

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

Deposited: 2016-10-11 Released: 2016-10-26
Deposition Author(s): Helliwell, J.R.
Funding Organization(s): Engineering and Physical Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.262 (Depositor)
R-Value Work:
0.216 (Depositor), 0.222 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The case of 1lkr held at the PDB and its variable amino acid occupancies; re refinement of 4ow9 to correct this

Helliwell, J.R., Tanley, S.W.M.

(2016) Zenodo

DOI: https://doi.org/10.5281/zenodo.160328

Macromolecule Content

Total Structure Weight: 33.15 kDa
Atom Count: 2,095
Modeled Residue Count: 258
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A, B	129	Gallus gallus	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT Query on PT Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], Z [auth B]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain Z [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain Z [auth B]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain HA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B]	HA [auth B] IA [auth B] JA [auth B] P [auth A] Q [auth A] HA [auth B], IA [auth B], JA [auth B], P [auth A], Q [auth A], R [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain KA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain KA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain KA [auth B]	KA [auth B], S [auth A], T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain KA [auth B] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain KA [auth B] Focus chain S [auth A] Focus chain T [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain LA [auth B] MOL2 format, chain LA [auth B] mmCIF format, chain LA [auth B]	LA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain LA [auth B] Interactions & Density Focus chain LA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.262 (Depositor)
R-Value Work: 0.216 (Depositor), 0.222 (DCC)
R-Value Observed: 0.218 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.251	α = 90
b = 62.537	β = 90.92
c = 58.981	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-10-26

Deposition Author(s):

Helliwell, J.R.

This entry supersedes: 4OW9

Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2016-10-26
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence
Version 1.2: 2019-07-17
Changes: Data collection, Derived calculations
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-09
Changes: Structure summary