8C7E | pdb_00008c7e

Serendipitous cyanase structure from Serratia-like contamination

PDB DOI: https://doi.org/10.2210/pdb8C7E/pdb

Classification: LYASE
Organism(s): unidentified
Mutation(s): No

Deposited: 2023-01-14 Released: 2023-02-22
Deposition Author(s): Bloch, Y., Skladanowska, K., Savvides, S.N.
Funding Organization(s): Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.236 (Depositor), 0.236 (DCC)
R-Value Work:
0.202 (Depositor), 0.201 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8C7E

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

Literature

Serendipitous cyanase structure from Serratia-like contamination.

Bloch, Y., Skladanowska, K., Savvides, S.N.

To be published.

Macromolecule Content

Total Structure Weight: 332.81 kDa
Atom Count: 23,339
Modeled Residue Count: 3,100
Deposited Residue Count: 3,100
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyanate hydratase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	155	unidentified	Mutation(s): 0 EC: 4.2.1.104
UniProt
Find proteins for A0A3E2EMR4 (Serratia marcescens) Explore A0A3E2EMR4 Go to UniProtKB: A0A3E2EMR4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3E2EMR4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain Y [auth D] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain NA [auth S] SDF format, chain MA [auth R] SDF format, chain LA [auth P] SDF format, chain KA [auth O] SDF format, chain JA [auth O] SDF format, chain IA [auth N] SDF format, chain HA [auth M] SDF format, chain GA [auth M] SDF format, chain FA [auth L] SDF format, chain EA [auth K] SDF format, chain DA [auth J] SDF format, chain CA [auth I] SDF format, chain BA [auth G] SDF format, chain AA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain NA [auth S] MOL2 format, chain MA [auth R] MOL2 format, chain LA [auth P] MOL2 format, chain KA [auth O] MOL2 format, chain JA [auth O] MOL2 format, chain IA [auth N] MOL2 format, chain HA [auth M] MOL2 format, chain GA [auth M] MOL2 format, chain FA [auth L] MOL2 format, chain EA [auth K] MOL2 format, chain DA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain NA [auth S] mmCIF format, chain MA [auth R] mmCIF format, chain LA [auth P] mmCIF format, chain KA [auth O] mmCIF format, chain JA [auth O] mmCIF format, chain IA [auth N] mmCIF format, chain HA [auth M] mmCIF format, chain GA [auth M] mmCIF format, chain FA [auth L] mmCIF format, chain EA [auth K] mmCIF format, chain DA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth G] CA [auth I] DA [auth J] EA [auth K] AA [auth F], BA [auth G], CA [auth I], DA [auth J], EA [auth K], FA [auth L], GA [auth M], HA [auth M], IA [auth N], JA [auth O], KA [auth O], LA [auth P], MA [auth R], NA [auth S], U [auth A], V [auth A], W [auth C], X [auth C], Y [auth D], Z [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain BA [auth G] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth M] Focus chain IA [auth N] Focus chain JA [auth O] Focus chain KA [auth O] Focus chain LA [auth P] Focus chain MA [auth R] Focus chain NA [auth S] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth G] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth M] Focus chain HA [auth M] Focus chain IA [auth N] Focus chain JA [auth O] Focus chain KA [auth O] Focus chain LA [auth P] Focus chain MA [auth R] Focus chain NA [auth S] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.236 (Depositor), 0.236 (DCC)
R-Value Work: 0.202 (Depositor), 0.201 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.121	α = 90
b = 90.121	β = 90
c = 736.358	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SIMBAD	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-22

Deposition Author(s):

Skladanowska, K.

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	12S0519N

Revision History (Full details and data files)

Version 1.0: 2023-02-22
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.