4HSF | pdb_00004hsf

Lysozyme with Arginine at 318K

PDB DOI: https://doi.org/10.2210/pdb4HSF/pdb

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

Deposited: 2012-10-30 Released: 2013-10-30
Deposition Author(s): Sharma, P., Ashish, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.225 (Depositor), 0.220 (DCC)
R-Value Work:
0.193 (Depositor), 0.180 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Lysozyme with Arginine at 318K.

Sharma, P., Ashish, F.

To be published.

Macromolecule Content

Total Structure Weight: 14.92 kDa
Atom Count: 1,121
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARG Query on ARG Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain G [auth A] mmCIF format, chain B [auth A] mmCIF format, chain G [auth A]	B [auth A], G [auth A]	ARGININE C₆ H₁₅ N₄ O₂ ODKSFYDXXFIFQN-BYPYZUCNSA-O		Interactions Focus chain B [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain G [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.225 (Depositor), 0.220 (DCC)
R-Value Work: 0.193 (Depositor), 0.180 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.353	α = 90
b = 78.353	β = 90
c = 37.063	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-10-30

Deposition Author(s):

Sharma, P.

Ashish, F.

Revision History (Full details and data files)

Version 1.0: 2013-10-30
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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Lysozyme with Arginine at 318K

Lysozyme with Arginine at 318K.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations