7F7D | pdb_00007f7d

Crystal structure of Non-specific class-C acid phosphatase from Sphingobium sp. RSMS bound to Adenosine at pH 5.5

PDB DOI: https://doi.org/10.2210/pdb7F7D/pdb

Classification: HYDROLASE
Organism(s): Sphingobium sp. 20006FA
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-06-28 Released: 2022-07-06
Deposition Author(s): Gaur, N.K., Kumar, A., Sunder, S., Mukhopadhyaya, R., Makde, R.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.202 (Depositor), 0.203 (DCC)
R-Value Work:
0.165 (Depositor), 0.166 (DCC)
R-Value Observed:
0.167 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Non-Specific Class-c acidphosphatase from Sphingobium sp. RSMS

Gaur, N.K., Kumar, A., Sunder, S., Mukhopadhyaya, R., Makde, R.D.

To be published.

Macromolecule Content

Total Structure Weight: 31.7 kDa
Atom Count: 2,079
Modeled Residue Count: 254
Deposited Residue Count: 296
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acid phosphatase	A	296	Sphingobium sp. 20006FA	Mutation(s): 0 Gene Names: A8O16_10785

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADN (Subject of Investigation/LOI) Query on ADN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.202 (Depositor), 0.203 (DCC)
R-Value Work: 0.165 (Depositor), 0.166 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.937	α = 90
b = 167.937	β = 90
c = 167.937	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MR-Rosetta	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Mukhopadhyaya, R.

Revision History (Full details and data files)

Version 1.0: 2022-07-06
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, 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.