3RT5 | pdb_00003rt5

Lysozyme in 30% propanol

PDB DOI: https://doi.org/10.2210/pdb3RT5/pdb

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

Deposited: 2011-05-03 Released: 2011-06-15
Deposition Author(s): Sharma, P., Solanki, A.K., Ashish

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.214 (Depositor), 0.215 (DCC)
R-Value Work:
0.183 (Depositor), 0.182 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Lysozyme in 30% propanol

Sharma, P., Solanki, A.K., Ashish

To be published.

Macromolecule Content

Total Structure Weight: 15.49 kDa
Atom Count: 1,142
Modeled Residue Count: 129
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 [auth X]	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
POL Query on POL Download:Ideal Coordinates CCD File SDF format, chain P [auth X] MOL2 format, chain P [auth X] mmCIF format, chain P [auth X]	P [auth X]	N-PROPANOL C₃ H₈ O BDERNNFJNOPAEC-UHFFFAOYSA-N		Interactions Focus chain P [auth X] Interactions & Density Focus chain P [auth X]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain O [auth X] SDF format, chain N [auth X] SDF format, chain M [auth X] SDF format, chain L [auth X] SDF format, chain K [auth X] SDF format, chain J [auth X] MOL2 format, chain O [auth X] MOL2 format, chain N [auth X] MOL2 format, chain M [auth X] MOL2 format, chain L [auth X] MOL2 format, chain K [auth X] MOL2 format, chain J [auth X] mmCIF format, chain O [auth X] mmCIF format, chain N [auth X] mmCIF format, chain M [auth X] mmCIF format, chain L [auth X] mmCIF format, chain K [auth X] mmCIF format, chain J [auth X]	J [auth X] K [auth X] L [auth X] M [auth X] N [auth X] J [auth X], K [auth X], L [auth X], M [auth X], N [auth X], O [auth X]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Focus chain N [auth X] Focus chain O [auth X] Interactions & Density Focus chain J [auth X] Focus chain K [auth X] Focus chain L [auth X] Focus chain M [auth X] Focus chain N [auth X] Focus chain O [auth X]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Q [auth X] MOL2 format, chain Q [auth X] mmCIF format, chain Q [auth X]	Q [auth X]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain Q [auth X] Interactions & Density Focus chain Q [auth X]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth X] SDF format, chain Y [auth X] SDF format, chain X SDF format, chain W [auth X] SDF format, chain V [auth X] SDF format, chain U [auth X] SDF format, chain T [auth X] SDF format, chain S [auth X] SDF format, chain R [auth X] SDF format, chain EA [auth X] SDF format, chain DA [auth X] SDF format, chain CA [auth X] SDF format, chain BA [auth X] SDF format, chain AA [auth X] MOL2 format, chain Z [auth X] MOL2 format, chain Y [auth X] MOL2 format, chain X MOL2 format, chain W [auth X] MOL2 format, chain V [auth X] MOL2 format, chain U [auth X] MOL2 format, chain T [auth X] MOL2 format, chain S [auth X] MOL2 format, chain R [auth X] MOL2 format, chain EA [auth X] MOL2 format, chain DA [auth X] MOL2 format, chain CA [auth X] MOL2 format, chain BA [auth X] MOL2 format, chain AA [auth X] mmCIF format, chain Z [auth X] mmCIF format, chain Y [auth X] mmCIF format, chain X mmCIF format, chain W [auth X] mmCIF format, chain V [auth X] mmCIF format, chain U [auth X] mmCIF format, chain T [auth X] mmCIF format, chain S [auth X] mmCIF format, chain R [auth X] mmCIF format, chain EA [auth X] mmCIF format, chain DA [auth X] mmCIF format, chain CA [auth X] mmCIF format, chain BA [auth X] mmCIF format, chain AA [auth X]	AA [auth X] BA [auth X] CA [auth X] DA [auth X] EA [auth X] AA [auth X], BA [auth X], CA [auth X], DA [auth X], EA [auth X], R [auth X], S [auth X], T [auth X], U [auth X], V [auth X], W [auth X], X, Y [auth X], Z [auth X]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth X] Focus chain BA [auth X] Focus chain CA [auth X] Focus chain DA [auth X] Focus chain EA [auth X] Focus chain R [auth X] Focus chain S [auth X] Focus chain T [auth X] Focus chain U [auth X] Focus chain V [auth X] Focus chain W [auth X] Focus chain X Focus chain Y [auth X] Focus chain Z [auth X] Interactions & Density Focus chain AA [auth X] Focus chain BA [auth X] Focus chain CA [auth X] Focus chain DA [auth X] Focus chain EA [auth X] Focus chain R [auth X] Focus chain S [auth X] Focus chain T [auth X] Focus chain U [auth X] Focus chain V [auth X] Focus chain W [auth X] Focus chain X Focus chain Y [auth X] Focus chain Z [auth X]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth X] SDF format, chain H [auth X] SDF format, chain G [auth X] SDF format, chain F [auth X] SDF format, chain E [auth X] SDF format, chain D [auth X] SDF format, chain C [auth X] SDF format, chain B [auth X] MOL2 format, chain I [auth X] MOL2 format, chain H [auth X] MOL2 format, chain G [auth X] MOL2 format, chain F [auth X] MOL2 format, chain E [auth X] MOL2 format, chain D [auth X] MOL2 format, chain C [auth X] MOL2 format, chain B [auth X] mmCIF format, chain I [auth X] mmCIF format, chain H [auth X] mmCIF format, chain G [auth X] mmCIF format, chain F [auth X] mmCIF format, chain E [auth X] mmCIF format, chain D [auth X] mmCIF format, chain C [auth X] mmCIF format, chain B [auth X]	B [auth X] C [auth X] D [auth X] E [auth X] F [auth X] B [auth X], C [auth X], D [auth X], E [auth X], F [auth X], G [auth X], H [auth X], I [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Interactions & Density Focus chain B [auth X] Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.214 (Depositor), 0.215 (DCC)
R-Value Work: 0.183 (Depositor), 0.182 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.935	α = 90
b = 77.935	β = 90
c = 36.961	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-06-15

Deposition Author(s):

Sharma, P.

Solanki, A.K.

Ashish

Revision History (Full details and data files)

Version 1.0: 2011-06-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary