3BDH | pdb_00003bdh

Crystal structure of zinc-deficient wild-type E. coli alkaline phosphatase

PDB DOI: https://doi.org/10.2210/pdb3BDH/pdb

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

Deposited: 2007-11-14 Released: 2008-11-18
Deposition Author(s): Grigg, J.C., Murphy, M.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.189 (Depositor), 0.190 (DCC)
R-Value Work:
0.152 (Depositor), 0.152 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

The Active-Site Trimetallic Cluster of Alkaline Phosphatase is Lost Upon Isosteric Mutation at the Mg2+-Coordinating Residue Threonine-155

Grigg, J.C., Hucaluk, C., Murphy, M.E., Ritter, H., Yee, J., Rafferty, S.

To be published.

Macromolecule Content

Total Structure Weight: 96.69 kDa
Atom Count: 7,751
Modeled Residue Count: 898
Deposited Residue Count: 916
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkaline phosphatase	A, B	458	Escherichia coli	Mutation(s): 0 Gene Names: phoA EC: 3.1.3.1
UniProt
Find proteins for P00634 (Escherichia coli (strain K12)) Explore P00634 Go to UniProtKB: P00634
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00634
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		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: 1.85 Å
R-Value Free: 0.189 (Depositor), 0.190 (DCC)
R-Value Work: 0.152 (Depositor), 0.152 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.449	α = 90
b = 103.545	β = 105.76
c = 88.489	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-11-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-11-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-13
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.