1QFX | pdb_00001qfx

PH 2.5 ACID PHOSPHATASE FROM ASPERGILLUS NIGER

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.225 (Depositor) 
  • R-Value Work: 
    0.183 (Depositor), 0.180 (DCC) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.2 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 Biology 288: 965-974

  • DOI: https://doi.org/10.1006/jmbi.1999.2736
  • Primary Citation 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 
  • Modeled Residue Count: 884 
  • Deposited Residue Count: 920 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (PH 2.5 ACID PHOSPHATASE)
A, B
460Aspergillus nigerMutation(s): 0 
EC: 3.1.3.8
UniProt
Find proteins for P34755 (Aspergillus awamori)
Explore P34755 
Go to UniProtKB:  P34755
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34755
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD 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
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G46836GH
GlyCosmos: G46836GH
GlyGen: G46836GH
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD 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
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG


Download:Ideal Coordinates CCD File
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
SO4

Query on SO4


Download:Ideal Coordinates CCD File
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
GOL

Query on GOL


Download:Ideal Coordinates CCD File
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.225 (Depositor) 
  • R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.6α = 90
b = 170.6β = 90
c = 201.15γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
SHELXSphasing
SHARPphasing
CCP4model building
X-PLORrefinement
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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
  • Version 2.2: 2024-11-13
    Changes: Structure summary