5IMG | pdb_00005img

C9A mutant of C69-family cysteine dipeptidase from Lactobacillus farciminis

PDB DOI: https://doi.org/10.2210/pdb5IMG/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: 1.84 Å
R-Value Free:
0.169 (Depositor), 0.170 (DCC)
R-Value Work:
0.138 (Depositor), 0.140 (DCC)
R-Value Observed:
0.139 (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: 529.92 kDa
Atom Count: 43,454
Modeled Residue Count: 4,670
Deposited Residue Count: 4,690
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 A, B, C, D, E, F, G, H, I, J	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain P [auth E] SDF format, chain U [auth G] SDF format, chain X [auth H] SDF format, chain W [auth H] SDF format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain P [auth E] MOL2 format, chain U [auth G] MOL2 format, chain X [auth H] MOL2 format, chain W [auth H] MOL2 format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain P [auth E] mmCIF format, chain U [auth G] mmCIF format, chain X [auth H] mmCIF format, chain W [auth H] mmCIF format, chain L [auth C]	K [auth C] L [auth C] P [auth E] U [auth G] W [auth H] K [auth C], L [auth C], P [auth E], U [auth G], W [auth H], X [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain L [auth C] Focus chain P [auth E] Focus chain U [auth G] Focus chain W [auth H] Focus chain X [auth H] Interactions & Density Focus chain K [auth C] Focus chain L [auth C] Focus chain P [auth E] Focus chain U [auth G] Focus chain W [auth H] Focus chain X [auth H]
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain Z [auth H] SDF format, chain V [auth G] SDF format, chain T [auth F] SDF format, chain S [auth F] SDF format, chain R [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain AA [auth J] MOL2 format, chain Y [auth H] MOL2 format, chain Z [auth H] MOL2 format, chain V [auth G] MOL2 format, chain T [auth F] MOL2 format, chain S [auth F] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain AA [auth J] mmCIF format, chain Y [auth H] mmCIF format, chain Z [auth H] mmCIF format, chain V [auth G] mmCIF format, chain T [auth F] mmCIF format, chain S [auth F] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain AA [auth J]	AA [auth J] M [auth C] N [auth C] O [auth D] Q [auth E] AA [auth J], M [auth C], N [auth C], O [auth D], Q [auth E], R [auth F], S [auth F], T [auth F], V [auth G], Y [auth H], Z [auth H]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth F] Focus chain V [auth G] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth J] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth F] Focus chain V [auth G] Focus chain Y [auth H] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.169 (Depositor), 0.170 (DCC)
R-Value Work: 0.138 (Depositor), 0.140 (DCC)
R-Value Observed: 0.139 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.944	α = 90
b = 182.788	β = 102.19
c = 158.523	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
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