5I5Q | pdb_00005i5q

Re refinement of 4mwn.

PDB DOI: https://doi.org/10.2210/pdb5I5Q/pdb
Entry: 5I5Q supersedes: 4MWN

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

Deposited: 2016-02-15 Released: 2016-05-18
Deposition Author(s): Helliwell, J.R.
Funding Organization(s): Engineering and Physical Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.237 (Depositor), 0.235 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4mwn

Literature

Comment on "Structural dynamics of cisplatin binding to histidine in a protein" [Struct. Dyn. 1, 034701 (2014)].

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

(2016) Struct Dyn 3: 037101-037101

PubMed: 27226979 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1063/1.4948613
Primary Citation Related Structures:
5HMV, 5HQ1, 5I5Q, 5IDD

Organizational Affiliation

School of Chemistry, University of Manchester , Manchester M13 9PL, United Kingdom.

Macromolecule Content

Total Structure Weight: 15.18 kDa
Atom Count: 1,057
Modeled Residue Count: 128
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT Query on PT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	C [auth A], G [auth A], H [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.237 (Depositor), 0.235 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)
R-Value Observed: 0.187 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.346	α = 88.04
b = 32.134	β = 71.17
c = 34.296	γ = 68.35

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
APEX	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-05-18

Deposition Author(s):

Helliwell, J.R.

This entry supersedes: 4MWN

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

Revision History (Full details and data files)

Version 1.0: 2016-05-18
Type: Initial release
Version 1.1: 2016-07-20
Changes: Database references
Version 1.2: 2017-09-13
Changes: Author supporting evidence, Data collection
Version 1.3: 2018-08-08
Changes: Data collection, Database references
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.5: 2024-11-13
Changes: Structure summary