9NPF | pdb_00009npf

Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b) from the GH2 family in the space group P1 at 2.15 A

PDB DOI: https://doi.org/10.2210/pdb9NPF/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: 2.15 Å
R-Value Free:
0.228 (Depositor), 0.229 (DCC)
R-Value Work:
0.207 (Depositor), 0.208 (DCC)
R-Value Observed:
0.208 (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) from the GH2 family in the space group P1 at 2.15 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: 554.48 kDa
Atom Count: 37,135
Modeled Residue Count: 4,397
Deposited Residue Count: 4,788
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 2	A, B, C, D, E A, B, C, D, E, F	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
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain LA [auth F] SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain W [auth C] SDF format, chain U [auth C] SDF format, chain O [auth B] SDF format, chain MA [auth F] SDF format, chain GA [auth E] SDF format, chain G [auth A] SDF format, chain FA [auth E] SDF format, chain EA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain W [auth C] MOL2 format, chain U [auth C] MOL2 format, chain O [auth B] MOL2 format, chain MA [auth F] MOL2 format, chain GA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain EA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain W [auth C] mmCIF format, chain U [auth C] mmCIF format, chain O [auth B] mmCIF format, chain MA [auth F] mmCIF format, chain GA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth E] mmCIF format, chain EA [auth E]	EA [auth E] FA [auth E] G [auth A] GA [auth E] H [auth A] EA [auth E], FA [auth E], G [auth A], GA [auth E], H [auth A], LA [auth F], MA [auth F], O [auth B], P [auth B], U [auth C], V [auth C], W [auth C], Y [auth D], Z [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain I [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain X [auth C] SDF format, chain Q [auth B] SDF format, chain NA [auth F] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth E] SDF format, chain K [auth A] SDF format, chain JA [auth E] SDF format, chain J [auth A] SDF format, chain IA [auth E] SDF format, chain HA [auth E] SDF format, chain CA [auth D] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain NA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain NA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] HA [auth E] AA [auth D], BA [auth D], CA [auth D], DA [auth D], HA [auth E], I [auth A], IA [auth E], J [auth A], JA [auth E], K [auth A], KA [auth E], L [auth A], M [auth A], NA [auth F], Q [auth B], R [auth B], S [auth B], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth F] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain T [auth B] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B] mmCIF format, chain N [auth A] mmCIF format, chain T [auth B]	N [auth A], T [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain N [auth A] Focus chain T [auth B] Interactions & Density Focus chain N [auth A] Focus chain T [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.228 (Depositor), 0.229 (DCC)
R-Value Work: 0.207 (Depositor), 0.208 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.703	α = 89.44
b = 123.566	β = 117.29
c = 133.238	γ = 103.2

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