9IQD | pdb_00009iqd

Apo-MicM,homologous of AkaM, SnoaL-like protein

PDB DOI: https://doi.org/10.2210/pdb9IQD/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Micromonospora sp. HM134
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-07-12 Released: 2025-07-16
Deposition Author(s): Zhang, B., Ge, H.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.181 (Depositor), 0.181 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9IQD

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

Literature

Structural and mechanistic insights into iminium-catalysed macrocyclization by nuclear transport factor 2-like enzymes

Liu, C.L., Zhang, B., Ge, H.M.

(2026) Nat Synth

DOI: https://doi.org/10.1038/s44160-025-00989-z

Macromolecule Content

Total Structure Weight: 59.15 kDa
Atom Count: 4,233
Modeled Residue Count: 477
Deposited Residue Count: 528
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SnoaL-like domain-containing protein	A, B, C, D	132	Micromonospora sp. HM134	Mutation(s): 0 Gene Names: FJK98_13695

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C]	G [auth A], J [auth B], O [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	E [auth A] F [auth A] H [auth A] I [auth B] K [auth B] E [auth A], F [auth A], H [auth A], I [auth B], K [auth B], L [auth C], M [auth C], P [auth C], R [auth D], S [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	Q [auth C], T [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain Q [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.216 (Depositor), 0.216 (DCC)
R-Value Work: 0.181 (Depositor), 0.181 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.306	α = 90
b = 72.732	β = 112.21
c = 65.403	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22277051,81925033, 22193071

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release
Version 1.1: 2026-02-04
Changes: Database references

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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.