7F0V | pdb_00007f0v

Structure of the M305I mutant of CueO

PDB DOI: https://doi.org/10.2210/pdb7F0V/pdb

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

Deposited: 2021-06-07 Released: 2022-06-15
Deposition Author(s): Kawano, T.K., Takata, S.T., Sakai, N.S., Imaizumi, R.I., Nakata, S.N., 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: 1.49 Å
R-Value Free:
0.232 (Depositor), 0.242 (DCC)
R-Value Work:
0.187 (Depositor), 0.195 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of the M305I mutant of CueO

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

To be published.

Macromolecule Content

Total Structure Weight: 114.24 kDa
Atom Count: 7,966
Modeled Residue Count: 949
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Blue copper oxidase CueO	A, B	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 J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	CU-O-CU LINKAGE Cu₂ O BERDEBHAJNAUOM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B]	F [auth A], G [auth A], K [auth B], M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A], D [auth A], H [auth B], I [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.232 (Depositor), 0.242 (DCC)
R-Value Work: 0.187 (Depositor), 0.195 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.798	α = 86.979
b = 49.922	β = 80.626
c = 95.933	γ = 70.535

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):

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
Version 1.2: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Derived calculations, Structure summary