1QFX

PH 2.5 ACID PHOSPHATASE FROM ASPERGILLUS NIGER

PDB DOI: https://doi.org/10.2210/pdb1QFX/pdb

Classification: HYDROLASE
Organism(s): Aspergillus niger
Mutation(s): No

Deposited: 1999-04-15 Released: 2000-04-19
Deposition Author(s): Kostrewa, D., Wyss, M., D'Arcy, A., Van Loon, A.P.G.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.225
R-Value Work: 0.183

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of Aspergillus niger pH 2.5 acid phosphatase at 2. 4 A resolution.

Kostrewa, D., Wyss, M., D'Arcy, A., van Loon, A.P.

(1999) J Mol Biol 288: 965-974

PubMed: 10329192 Search on PubMed
DOI: https://doi.org/10.1006/jmbi.1999.2736
Primary Citation of Related Structures:
1QFX

PubMed Abstract:
The crystal structure of Aspergillus niger pH 2.5 acid phosphatase (EC 3.1.3.2) has been determined at 2.4 A resolution. In the crystal, two dimers form a tetramer in which the active sites are easily accessible to substrates. The main contacts in the dimer come from the N termini, each lying on the surface of the neighbouring molecule. The monomer consists of two domains, with the active site located at their interface. The active site has a highly conserved catalytic center and a charge distribution, which explains the highly acidic pH optimum and the broad substrate specificity of the enzyme.

Organizational Affiliation

F. Hoffmann-La Roche Ltd, B/65/R312, Basel, 4070, Switzerland. dirk.kostrewa@roche.com

Macromolecule Content

Total Structure Weight: 106.4 kDa
Atom Count: 7,835
Modelled Residue Count: 884
Deposited Residue Count: 920
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PH 2.5 ACID PHOSPHATASE)	A, B	460	Aspergillus niger	Mutation(s): 0 EC: 3.1.3.8
UniProt
Find proteins for P34755 (Aspergillus awamori) Explore P34755 Go to UniProtKB: P34755
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P34755
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	7		N-Glycosylation	Interactions Focus chain C
Glycosylation Resources
GlyTouCan: G46836GH GlyCosmos: G46836GH GlyGen: G46836GH

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	5		N-Glycosylation	Interactions Focus chain D
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	E [auth A], F [auth A], O [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	L [auth A] M [auth A] N [auth A] W [auth B] X [auth B] L [auth A], M [auth A], N [auth A], W [auth B], X [auth B], Y [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.225
R-Value Work: 0.183
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.6	α = 90
b = 170.6	β = 90
c = 201.15	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
SHELXS	phasing
SHARP	phasing
CCP4	model building
X-PLOR	refinement
CCP4	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2000-04-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-04-19
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-12-27
Changes: Data collection, Database references, Structure summary

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Help and Resources

1QFX

PH 2.5 ACID PHOSPHATASE FROM ASPERGILLUS NIGER

Crystal structure of Aspergillus niger pH 2.5 acid phosphatase at 2. 4 A resolution.

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

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Entity ID: 2

Glycosylation Resources