3DKU | pdb_00003dku

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1

PDB DOI: https://doi.org/10.2210/pdb3DKU/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli APEC O1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-26 Released: 2009-06-30
Deposition Author(s): Hong, M.K., Kim, J.K., Jung, J.H., Jung, J.W., Choi, J.Y., Kang, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free:
0.270 (Depositor), 0.269 (DCC)
R-Value Work:
0.193 (Depositor), 0.194 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1.

Hong, M.K., Kim, J.K., Jung, J.H., Jung, J.W., Choi, J.Y., Kang, L.W.

To be published.

Macromolecule Content

Total Structure Weight: 139.61 kDa
Atom Count: 9,800
Modeled Residue Count: 1,201
Deposited Residue Count: 1,224
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phosphohydrolase	A, B, C, D, E A, B, C, D, E, F, G, H	153	Escherichia coli APEC O1	Mutation(s): 0 EC: 3.6.1
UniProt
Find proteins for A1AA28 (Escherichia coli O1:K1 / APEC) Explore A1AA28 Go to UniProtKB: A1AA28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1AA28
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.270 (Depositor), 0.269 (DCC)
R-Value Work: 0.193 (Depositor), 0.194 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.96	α = 90
b = 70.521	β = 103.3
c = 145.031	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence
Version 1.3: 2019-12-25
Changes: Derived calculations
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Refinement description

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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.