5R47

Crystal Structure of deuterated gamma-Chymotrypsin at pH 5.6, cryo temperature

PDB DOI: https://doi.org/10.2210/pdb5R47/pdb
Deposition Group: G_1002095 ExploreG_1002095

Classification: HYDROLASE
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2020-02-18 Released: 2021-09-01
Deposition Author(s): Kreinbring, C.A., Wilson, M.A., Kovalevsky, A.Y., Blakeley, M.P., Fisher, S.Z., Lazar, L.M., Moulin, A.G., Novak, W.R., Petsko, G.A., Ringe, D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.131
R-Value Work: 0.119
R-Value Observed: 0.120

wwPDB Validation 3D Report Full Report

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

Literature

Effect of Temperature and pH on Ionizable Residues in gamma-Chymotrypsin: a X-ray and Neutron Crystallography Study

Kreinbring, C.A., Wilson, M.A., Kovalevsky, A.Y., Blakeley, M.P., Fisher, S.Z., Lazar, L.M., Moulin, A.G., Novak, W.R., Petsko, G.A., Ringe, D.

To be published.

Macromolecule Content

Total Structure Weight: 26.71 kDa
Atom Count: 2,290
Modelled Residue Count: 247
Deposited Residue Count: 250
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gamma-chymotrypsin	A	13	Bos taurus	Mutation(s): 0 EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus) Explore P00766 Go to UniProtKB: P00766
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00766
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
gamma-chymotrypsin	B	131	Bos taurus	Mutation(s): 0 EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus) Explore P00766 Go to UniProtKB: P00766
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00766
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
gamma-chymotrypsin	C	97	Bos taurus	Mutation(s): 0 EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus) Explore P00766 Go to UniProtKB: P00766
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00766
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide SWPW	D	4	Bos taurus	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide TPGVY	E	5	Bos taurus	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth C]	F [auth A], H [auth C]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.131
R-Value Work: 0.119
R-Value Observed: 0.120
Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.525	α = 90
b = 68.525	β = 90
c = 96.685	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-09-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM32415
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM26788