5IMH | pdb_00005imh

D31P mutant of C69-family cysteine dipeptidase from Lactobacillus farciminis

PDB DOI: https://doi.org/10.2210/pdb5IMH/pdb

Classification: HYDROLASE
Organism(s): Companilactobacillus farciminis KCTC 3681 = DSM 20184
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-03-06 Released: 2017-03-15
Deposition Author(s): Kono, R., Watanabe, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.188 (Depositor), 0.190 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

A C69-family cysteine dipeptidase from Lactobacillus farciminis; substrate recognition mechanism and autoproteolytic mechanism in enzyme maturation

Kono, R., Watanabe, K.

To be published.

Macromolecule Content

Total Structure Weight: 265.21 kDa
Atom Count: 19,121
Modeled Residue Count: 2,335
Deposited Residue Count: 2,345
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidase	A, B, C, D, E	469	Companilactobacillus farciminis KCTC 3681 = DSM 20184	Mutation(s): 1 Gene Names: FC68_GL001211
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A], O [auth C], P [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth C] Focus chain P [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] K [auth B] M [auth C] N [auth C] F [auth A], G [auth A], K [auth B], M [auth C], N [auth C], Q [auth D], R [auth E]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.188 (Depositor), 0.190 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.337	α = 90
b = 137.088	β = 100.75
c = 101.297	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-03-15

Deposition Author(s):

Kono, R.

Watanabe, K.

Revision History (Full details and data files)

Version 1.0: 2017-03-15
Type: Initial release
Version 1.1: 2019-11-20
Changes: Data collection, Derived calculations
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description