9NPD | pdb_00009npd

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E553Q Mutant) from the GH2 family in the space group P3121 at 3.05 A

PDB DOI: https://doi.org/10.2210/pdb9NPD/pdb

Classification: HYDROLASE
Organism(s): metagenome
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-03-11 Released: 2025-11-12
Deposition Author(s): Martins, M.P., Spadeto, J.P.M., Miyamoto, R.Y., Morais, M.A.B., Murakami, M.T.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free:
0.238 (Depositor), 0.239 (DCC)
R-Value Work:
0.217 (Depositor), 0.219 (DCC)
R-Value Observed:
0.219 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E553Q Mutant) from the GH2 family in the space group P3121 at 3.05 A

Martins, M.P., Spadeto, J.P.M., Miyamoto, R.Y., Morais, M.A.B., Murakami, M.T.

To be published.

Macromolecule Content

Total Structure Weight: 273.78 kDa
Atom Count: 17,910
Modeled Residue Count: 2,212
Deposited Residue Count: 2,394
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 2	A, B, C	798	metagenome	Mutation(s): 0 EC: 3.2.1.25
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
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	L [auth B], M [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain L [auth B] Focus chain M [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain P [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain P [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain P [auth C]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], N [auth C], O [auth C], P [auth C], Q [auth C], R [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B]	G [auth A], H [auth A], K [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.238 (Depositor), 0.239 (DCC)
R-Value Work: 0.217 (Depositor), 0.219 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 222.906	α = 90
b = 222.906	β = 90
c = 151.36	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2021/04891-3
Sao Paulo Research Foundation (FAPESP)	Brazil	2021/09793-0
Sao Paulo Research Foundation (FAPESP)	Brazil	2022/06298-0