4NPR | pdb_00004npr

Crystal Structure of the Family 12 Xyloglucanase from Aspergillus niveus

PDB DOI: https://doi.org/10.2210/pdb4NPR/pdb

Classification: HYDROLASE
Organism(s): Aspergillus niveus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-11-22 Released: 2014-12-24
Deposition Author(s): Cordeiro, R.L., Santos, C.R., Furtado, G.P., Damasio, A.R.L., Polizeli, M.L.T.M., Ward, R.J., Murakami, M.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.242 (Depositor), 0.245 (DCC)
R-Value Work:
0.186 (Depositor), 0.194 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of the Family 12 Xyloglucanase from Aspergillus niveus

Santos, C.R., Cordeiro, R.L., Furtado, G.P., Damasio, A.R.L., Polizeli, M.L.T.M., Ward, R.J., Murakami, M.T.

To be published.

Macromolecule Content

Total Structure Weight: 52.27 kDa
Atom Count: 3,388
Modeled Residue Count: 440
Deposited Residue Count: 486
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xyloglucan-specific endo-beta-1,4-glucanase GH12	A, B	243	Aspergillus niveus	Mutation(s): 0 EC: 3.2.1.151
UniProt
Find proteins for H6TQN1 (Aspergillus niveus) Explore H6TQN1 Go to UniProtKB: H6TQN1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H6TQN1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.242 (Depositor), 0.245 (DCC)
R-Value Work: 0.186 (Depositor), 0.194 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.368	α = 90
b = 62.368	β = 90
c = 226.037	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-12-24

Deposition Author(s):

Damasio, A.R.L.

Polizeli, M.L.T.M.

Revision History (Full details and data files)

Version 1.0: 2014-12-24
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

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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.