3SHD | pdb_00003shd

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

PDB DOI: https://doi.org/10.2210/pdb3SHD/pdb

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

Deposited: 2011-06-16 Released: 2012-06-27
Deposition Author(s): Hong, M.K., Kim, J.K., Kang, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.291 (Depositor), 0.288 (DCC)
R-Value Work:
0.226 (Depositor), 0.224 (DCC)
R-Value Observed:
0.230 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3SHD

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

Literature

Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

Hong, M.K.

To be published.

Macromolecule Content

Total Structure Weight: 214.19 kDa
Atom Count: 14,985
Modeled Residue Count: 1,800
Deposited Residue Count: 1,836
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatase nudJ	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	153	Escherichia coli APEC O1	Mutation(s): 0 Gene Names: nudJ, Ecok1_10240, APECO1_216 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain ZA [auth H] SDF format, chain Z [auth C] SDF format, chain YA [auth H] SDF format, chain Y [auth C] SDF format, chain XA [auth H] SDF format, chain V [auth B] SDF format, chain UA [auth G] SDF format, chain U [auth B] SDF format, chain TB [auth L] SDF format, chain TA [auth G] SDF format, chain T [auth B] SDF format, chain SB [auth L] SDF format, chain SA [auth G] SDF format, chain RB [auth L] SDF format, chain Q [auth A] SDF format, chain PA [auth F] SDF format, chain P [auth A] SDF format, chain OB [auth K] SDF format, chain OA [auth F] SDF format, chain O [auth A] SDF format, chain NB [auth K] SDF format, chain NA [auth F] SDF format, chain MB [auth K] SDF format, chain KA [auth E] SDF format, chain JB [auth J] SDF format, chain JA [auth E] SDF format, chain IB [auth J] SDF format, chain IA [auth E] SDF format, chain HB [auth J] SDF format, chain FA [auth D] SDF format, chain EB [auth I] SDF format, chain EA [auth D] SDF format, chain DB [auth I] SDF format, chain DA [auth D] SDF format, chain CB [auth I] SDF format, chain AA [auth C] MOL2 format, chain ZA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain Y [auth C] MOL2 format, chain XA [auth H] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain U [auth B] MOL2 format, chain TB [auth L] MOL2 format, chain TA [auth G] MOL2 format, chain T [auth B] MOL2 format, chain SB [auth L] MOL2 format, chain SA [auth G] MOL2 format, chain RB [auth L] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth K] MOL2 format, chain OA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain NB [auth K] MOL2 format, chain NA [auth F] MOL2 format, chain MB [auth K] MOL2 format, chain KA [auth E] MOL2 format, chain JB [auth J] MOL2 format, chain JA [auth E] MOL2 format, chain IB [auth J] MOL2 format, chain IA [auth E] MOL2 format, chain HB [auth J] MOL2 format, chain FA [auth D] MOL2 format, chain EB [auth I] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth I] MOL2 format, chain DA [auth D] MOL2 format, chain CB [auth I] MOL2 format, chain AA [auth C] mmCIF format, chain ZA [auth H] mmCIF format, chain Z [auth C] mmCIF format, chain YA [auth H] mmCIF format, chain Y [auth C] mmCIF format, chain XA [auth H] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth G] mmCIF format, chain U [auth B] mmCIF format, chain TB [auth L] mmCIF format, chain TA [auth G] mmCIF format, chain T [auth B] mmCIF format, chain SB [auth L] mmCIF format, chain SA [auth G] mmCIF format, chain RB [auth L] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth K] mmCIF format, chain OA [auth F] mmCIF format, chain O [auth A] mmCIF format, chain NB [auth K] mmCIF format, chain NA [auth F] mmCIF format, chain MB [auth K] mmCIF format, chain KA [auth E] mmCIF format, chain JB [auth J] mmCIF format, chain JA [auth E] mmCIF format, chain IB [auth J] mmCIF format, chain IA [auth E] mmCIF format, chain HB [auth J] mmCIF format, chain FA [auth D] mmCIF format, chain EB [auth I] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth I] mmCIF format, chain DA [auth D] mmCIF format, chain CB [auth I] mmCIF format, chain AA [auth C]	AA [auth C] CB [auth I] DA [auth D] DB [auth I] EA [auth D] AA [auth C], CB [auth I], DA [auth D], DB [auth I], EA [auth D], EB [auth I], FA [auth D], HB [auth J], IA [auth E], IB [auth J], JA [auth E], JB [auth J], KA [auth E], MB [auth K], NA [auth F], NB [auth K], O [auth A], OA [auth F], OB [auth K], P [auth A], PA [auth F], Q [auth A], RB [auth L], SA [auth G], SB [auth L], T [auth B], TA [auth G], TB [auth L], U [auth B], UA [auth G], V [auth B], XA [auth H], Y [auth C], YA [auth H], Z [auth C], ZA [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain CB [auth I] Focus chain DA [auth D] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain EB [auth I] Focus chain FA [auth D] Focus chain HB [auth J] Focus chain IA [auth E] Focus chain IB [auth J] Focus chain JA [auth E] Focus chain JB [auth J] Focus chain KA [auth E] Focus chain MB [auth K] Focus chain NA [auth F] Focus chain NB [auth K] Focus chain O [auth A] Focus chain OA [auth F] Focus chain OB [auth K] Focus chain P [auth A] Focus chain PA [auth F] Focus chain Q [auth A] Focus chain RB [auth L] Focus chain SA [auth G] Focus chain SB [auth L] Focus chain T [auth B] Focus chain TA [auth G] Focus chain TB [auth L] Focus chain U [auth B] Focus chain UA [auth G] Focus chain V [auth B] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain CB [auth I] Focus chain DA [auth D] Focus chain DB [auth I] Focus chain EA [auth D] Focus chain EB [auth I] Focus chain FA [auth D] Focus chain HB [auth J] Focus chain IA [auth E] Focus chain IB [auth J] Focus chain JA [auth E] Focus chain JB [auth J] Focus chain KA [auth E] Focus chain MB [auth K] Focus chain NA [auth F] Focus chain NB [auth K] Focus chain O [auth A] Focus chain OA [auth F] Focus chain OB [auth K] Focus chain P [auth A] Focus chain PA [auth F] Focus chain Q [auth A] Focus chain RB [auth L] Focus chain SA [auth G] Focus chain SB [auth L] Focus chain T [auth B] Focus chain TA [auth G] Focus chain TB [auth L] Focus chain U [auth B] Focus chain UA [auth G] Focus chain V [auth B] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain WA [auth H] SDF format, chain W [auth C] SDF format, chain VA [auth H] SDF format, chain S [auth B] SDF format, chain RA [auth G] SDF format, chain R [auth B] SDF format, chain QB [auth L] SDF format, chain QA [auth G] SDF format, chain PB [auth L] SDF format, chain N [auth A] SDF format, chain MA [auth F] SDF format, chain M [auth A] SDF format, chain LB [auth K] SDF format, chain LA [auth F] SDF format, chain KB [auth K] SDF format, chain HA [auth E] SDF format, chain GB [auth J] SDF format, chain GA [auth E] SDF format, chain FB [auth J] SDF format, chain CA [auth D] SDF format, chain BB [auth I] SDF format, chain BA [auth D] SDF format, chain AB [auth I] MOL2 format, chain X [auth C] MOL2 format, chain WA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain QB [auth L] MOL2 format, chain QA [auth G] MOL2 format, chain PB [auth L] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth K] MOL2 format, chain LA [auth F] MOL2 format, chain KB [auth K] MOL2 format, chain HA [auth E] MOL2 format, chain GB [auth J] MOL2 format, chain GA [auth E] MOL2 format, chain FB [auth J] MOL2 format, chain CA [auth D] MOL2 format, chain BB [auth I] MOL2 format, chain BA [auth D] MOL2 format, chain AB [auth I] mmCIF format, chain X [auth C] mmCIF format, chain WA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain VA [auth H] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain QB [auth L] mmCIF format, chain QA [auth G] mmCIF format, chain PB [auth L] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth K] mmCIF format, chain LA [auth F] mmCIF format, chain KB [auth K] mmCIF format, chain HA [auth E] mmCIF format, chain GB [auth J] mmCIF format, chain GA [auth E] mmCIF format, chain FB [auth J] mmCIF format, chain CA [auth D] mmCIF format, chain BB [auth I] mmCIF format, chain BA [auth D] mmCIF format, chain AB [auth I]	AB [auth I] BA [auth D] BB [auth I] CA [auth D] FB [auth J] AB [auth I], BA [auth D], BB [auth I], CA [auth D], FB [auth J], GA [auth E], GB [auth J], HA [auth E], KB [auth K], LA [auth F], LB [auth K], M [auth A], MA [auth F], N [auth A], PB [auth L], QA [auth G], QB [auth L], R [auth B], RA [auth G], S [auth B], VA [auth H], W [auth C], WA [auth H], X [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain BA [auth D] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain KB [auth K] Focus chain LA [auth F] Focus chain LB [auth K] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain PB [auth L] Focus chain QA [auth G] Focus chain QB [auth L] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain VA [auth H] Focus chain W [auth C] Focus chain WA [auth H] Focus chain X [auth C] Interactions & Density Focus chain AB [auth I] Focus chain BA [auth D] Focus chain BB [auth I] Focus chain CA [auth D] Focus chain FB [auth J] Focus chain GA [auth E] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain KB [auth K] Focus chain LA [auth F] Focus chain LB [auth K] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain PB [auth L] Focus chain QA [auth G] Focus chain QB [auth L] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain VA [auth H] Focus chain W [auth C] Focus chain WA [auth H] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.291 (Depositor), 0.288 (DCC)
R-Value Work: 0.226 (Depositor), 0.224 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.126	α = 90
b = 111.126	β = 90
c = 247.306	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-06-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-27
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.