7F19 | pdb_00007f19

Structure of the G304E mutant of CueO

PDB DOI: https://doi.org/10.2210/pdb7F19/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-06-08 Released: 2022-06-15
Deposition Author(s): Takata, S.T., Kawano, T.K., Nakata, S.N., Takado, K.T., Imaizumi, R.I., Sakai, N.S., Takeshita, K.T., Yamashita, S.Y., Sakurai, T.S., Kataoka, K.K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.253 (Depositor)
R-Value Work:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7F19

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

Literature

Structure of the G304E mutant of CueO

Takata, S.T., Kawano, T.K., Nakata, S.N., Takado, K.T., Imaizumi, R.I., Sakai, N.S., Takeshita, K.T., Yamashita, S.Y., Sakurai, T.S., Kataoka, K.K.

To be published.

Macromolecule Content

Total Structure Weight: 57.58 kDa
Atom Count: 3,659
Modeled Residue Count: 444
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Blue copper oxidase CueO	A	516	Escherichia coli	Mutation(s): 1 Gene Names: cueO, A9R57_04170, AUQ13_07730, BANRA_00502, BANRA_02318, BANRA_03294, BHS87_00550, BJJ90_21590, BMA87_12960, BUE81_03880... cueO, A9R57_04170, AUQ13_07730, BANRA_00502, BANRA_02318, BANRA_03294, BHS87_00550, BJJ90_21590, BMA87_12960, BUE81_03880, BvCms2454_01631, BvCmsHHP056_04875, BvCmsKKP036_02792, BvCmsKSP026_04756, BvCmsSINP011_00803, BW690_21865, C5F72_22005, C5F73_07705, C5N07_08325, C6669_04510, C9E25_07140, CA593_03120, CG692_01085, CI693_14840, CWS33_09370, D0X26_09670, D3821_05970, D6T60_04275, D9C99_10035, D9D44_07015, D9I18_13120, D9J11_09660, D9J52_04795, D9Z28_05630, DAH34_04440, DJ503_00645, DNC98_11530, DT034_05590, E2119_07645, E2134_11740, E2135_03380, E4K53_07200, E4K55_07200, E4K61_10655, E5P28_13255, E5S44_09260, EA213_09430, EAI42_26240, EAI46_26365, EAI52_02170, EC1094V2_3732, EC3234A_2c01050, ECTO6_03944, EEP23_00405, EG808_12120, EI021_04575, EI041_03395, EJC75_22495, EL75_3641, EL79_3751, EL80_3698, EPT01_02830, ERS150873_01065, ETECE1441_03949, EYD11_18775, EYV18_05255, EYY78_13140, FRV13_02155, FV293_03130, G5632_10235, G5688_04010, G5696_01080, G9P49_18255, GHD50_13365, GKF39_00960, GKF74_00135, GKF86_00960, GKF89_02255, GKG12_02350, GQE22_02395, GQE33_14025, GQE34_09055, GQE42_19525, GQE64_01625, GQM04_26830, GRW02_08355, GRW05_24815, GRW57_18925, GRW80_09165, GRW81_09580, H4P50_20865, H4P51_20715, HH707_001039, HLT96_06715, HLU13_04335, HMQ05_02945, HNC40_15140, HNC94_15135, HNN86_16410, HPE39_04120, HV005_17560, HV022_19655, HV068_19765, HV109_19610, HVX22_18960, HVY77_21410, HVY79_03855, HVY93_19425, HVZ24_18700, HVZ62_10495, HX136_20845, NCTC11022_04845, NCTC9045_04770, NCTC9058_02748, NCTC9062_04168, NCTC9706_01385, RK56_013325, SAMEA3472043_02481, SAMEA3472070_02440, SAMEA3484427_01313, SAMEA3484429_01168, SAMEA3752557_00827, SAMEA3752559_03758, SAMEA3753300_01926, SK85_00121, WP2S18E08_38200, WP7S17E04_36210, WQ89_09325 EC: 1 (PDB Primary Data), 1.16.3.4 (UniProt)
UniProt
Find proteins for P36649 (Escherichia coli (strain K12)) Explore P36649 Go to UniProtKB: P36649
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36649
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2O Query on C2O 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]	CU-O-CU LINKAGE Cu₂ O BERDEBHAJNAUOM-UHFFFAOYSA-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 F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], K [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.253 (Depositor)
R-Value Work: 0.206 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.892	α = 90
b = 62.287	β = 96.153
c = 96.653	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
XSCALE	data scaling
BALBES	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-15

Deposition Author(s):

Takeshita, K.T.

Yamashita, S.Y.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K05432
Japan Agency for Medical Research and Development (AMED)	Japan	BINDS1842

Revision History (Full details and data files)

Version 1.0: 2022-06-15
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Derived calculations, 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.