5AC3

Crystal structure of PAM12A

PDB DOI: https://doi.org/10.2210/pdb5AC3/pdb

Classification: HYDROLASE
Organism(s): Stenotrophomonas maltophilia
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2015-08-11 Released: 2016-07-20
Deposition Author(s): Wu, B., Wijma, H.J., Song, L., Rozeboom, H.J., Poloni, C., Tian, Y., Arif, M.I., Nuijens, T., Quadflieg, P.J.L.M., Szymanski, W., Feringa, B.L., Janssen, D.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.196 (Depositor), 0.200 (DCC)
R-Value Work:
0.160 (Depositor), 0.170 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Versatile Peptide C-Terminal Functionalization Via a Computationally Peptide Amidase

Wu, B., Wijma, H.J., Song, L., Rozeboom, H.J., Poloni, C., Tian, Y., Arif, M.I., Nuijens, T., Quadflieg, P.J.L.M., Szymanski, W., Feringa, B.L., Janssen, D.B.

(2016) ACS Catal

DOI: https://doi.org/10.1021/ACSCATAL.6B01062

Macromolecule Content

Total Structure Weight: 56.3 kDa
Atom Count: 4,061
Modelled Residue Count: 490
Deposited Residue Count: 514
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE AMIDASE	A	514	Stenotrophomonas maltophilia	Mutation(s): 12 EC: 3.5.1.4
UniProt
Find proteins for Q8RJN5 (Stenotrophomonas maltophilia) Explore Q8RJN5 Go to UniProtKB: Q8RJN5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RJN5
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain B [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] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain B [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] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.196 (Depositor), 0.200 (DCC)
R-Value Work: 0.160 (Depositor), 0.170 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.87	α = 90
b = 82.87	β = 90
c = 112.891	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-07-20
Type: Initial release
Version 1.1: 2017-07-05
Changes: Data collection
Version 1.2: 2019-01-30
Changes: Data collection, Experimental preparation
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-10-23
Changes: Structure summary