PDB-9kvm: Neutron and X-ray joint refined structure of a copper-containing ...

ID or keywords:

Entry

Database: PDB / ID: 9kvm

Title

Neutron and X-ray joint refined structure of a copper-containing nitrite reductase (C135A mutant) in complex with formate

Components

Copper-containing nitrite reductase

Keywords

OXIDOREDUCTASE / copper / denitrification

Function / homology

Function and homology information

nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / copper ion binding
Similarity search - Function

Biological species

Geobacillus thermodenitrificans (bacteria)

Method

X-RAY DIFFRACTION / NEUTRON DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.2 Å

Authors

Fukuda, Y. / Lintuluoto, M. / Hirano, Y. / Kusaka, K. / Inoue, T. / Tamada, T.

Funding support

Japan, 1items

Citation

Journal: J.Biol.Chem. / Year: 2025
Title: Structural basis of cuproenzyme nitrite reduction at the level of a single hydrogen atom.
Authors: Fukuda, Y. / Lintuluoto, M. / Hirano, Y. / Kusaka, K. / Inoue, T. / Tamada, T.

History

Deposition	Dec 5, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 11, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9kvm.cif.gz	236.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9kvm.ent.gz	175.9 KB	Display	PDB format
PDBx/mmJSON format	9kvm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kv/9kvm ftp://data.pdbj.org/pub/pdb/validation_reports/kv/9kvm	HTTPS FTP

-
Related structure data

Related structure data	9kvlC 9kwsC 9kwtC 9kwuC 9kwvC 4ysoS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Copper-containing nitrite reductase

hetero molecules

35.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Copper-containing nitrite reductase

hetero molecules

A: Copper-containing nitrite reductase

hetero molecules

A: Copper-containing nitrite reductase

hetero molecules

defined by author&software
107 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	116.172, 116.172, 85.612
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3
Space group name Hall	R3
Symmetry operation	#1: x,y,z #2: -y,x-y,z #3: -x+y,-x,z #4: x+1/3,y+2/3,z+2/3 #5: -y+1/3,x-y+2/3,z+2/3 #6: -x+y+1/3,-x+2/3,z+2/3 #7: x+2/3,y+1/3,z+1/3 #8: -y+2/3,x-y+1/3,z+1/3 #9: -x+y+2/3,-x+1/3,z+1/3

Components on special symmetry positions

ID	Model	Components
1	1	A-717- HOH
2	1	A-722- HOH
3	1	A-722- HOH
4	1	A-726- HOH
5	1	A-727- HOH

#1: Protein	Copper-containing nitrite reductase Mass: 35490.996 Da / Num. of mol.: 1 / Mutation: C135A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans (strain NG80-2) (bacteria) Gene: nirK, GTNG_0650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4IL26, nitrite reductase (NO-forming)
#2: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

Experiment

Method	Number of used crystals
X-RAY DIFFRACTION	1
NEUTRON DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 3.13 Å³/Da / Density % sol: 60.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M acetate buffer pH 4.5, 5.5% (w/v) PEG 4000, and 75 mM CuSO4

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	298	1	N
2	298	1	N

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SPALLATION SOURCE	JPARC MLF	BL-03	J-PARC MLF BEAMLINE BL-03	1	2.44-5.28
SYNCHROTRON	Photon Factory	BL-5A		2	1

Detector

Type	ID	Detector	Date
iBIX	1	DIFFRACTOMETER	May 13, 2021
DECTRIS PILATUS3 S 6M	2	PIXEL	Jul 1, 2021

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	LAUE	L	neutron	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	2.44	1
2	5.28	1
3	1	1

Reflection

B_iso Wilson estimate: 12.78 Å² / Entry-ID: 9KVM

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	CC_1/2	R_merge(I) obs	R_pim(I) all	Diffraction-ID	Net I/σ(I)
1.9-20	33212	97.7	6.8	0.975	0.264	0.108	1	6.5
1.2-43.4	134752	100	5.1	0.996	0.088	0.021	2	9.7

Reflection shell

Mean I/σ(I) obs: 1.7

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	Diffraction-ID	% possible all
1.9-2	5.1	0.89	4926	0.527	0.428	1	99.5
1.2-1.22	5	0.9	6689	0.701	0.253	2	100

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
STARGazer		data reduction
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

SU ML: 0.0888 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 18.9096 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 4YSO

4yso

/ Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)	Refine-ID	B_iso mean (Å²)	R_factor R_free	R_factor R_work	R_factor obs	Num. reflection R_free	Num. reflection R_work	Num. reflection obs	% reflection R_free (%)	% reflection obs (%)	Diffraction-ID	σ(F)
1.2-39.39	X-RAY DIFFRACTION	30	0.1185	0.1139	0.1141	3999	130743	134742	2.97	99.98	2	1.97
1.9-12.9	NEUTRON DIFFRACTION		0.183	0.146				33208		96.94	1

Refinement step

Cycle: LAST / Resolution: 1.2→39.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2335	0	7	227	2569

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0217	5482
X-RAY DIFFRACTION	f_angle_d	1.1745	9475
X-RAY DIFFRACTION	f_chiral_restr	0.0908	390
X-RAY DIFFRACTION	f_plane_restr	0.0065	891
X-RAY DIFFRACTION	f_dihedral_angle_d	16.5797	1465

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.2-1.21	0.2596	92	0.25	4600	X-RAY DIFFRACTION	100
1.21-1.23	0.2068	91	0.2368	4480	X-RAY DIFFRACTION	100
1.23-1.24	0.2777	91	0.2184	4558	X-RAY DIFFRACTION	100
1.24-1.26	0.2245	90	0.2103	4629	X-RAY DIFFRACTION	100
1.26-1.28	0.2307	93	0.1881	4554	X-RAY DIFFRACTION	99.98
1.28-1.3	0.1973	92	0.1793	4527	X-RAY DIFFRACTION	100
1.3-1.32	0.1534	92	0.1709	4518	X-RAY DIFFRACTION	100
1.32-1.34	0.2039	93	0.1638	4604	X-RAY DIFFRACTION	99.98
1.34-1.36	0.1774	91	0.1595	4533	X-RAY DIFFRACTION	99.91
1.36-1.38	0.1556	91	0.1519	4550	X-RAY DIFFRACTION	99.91
1.38-1.41	0.148	90	0.1473	4552	X-RAY DIFFRACTION	100
1.41-1.43	0.1642	94	0.1397	4556	X-RAY DIFFRACTION	99.98
1.43-1.46	0.1582	89	0.1352	4541	X-RAY DIFFRACTION	100
1.46-1.49	0.1554	92	0.1354	4545	X-RAY DIFFRACTION	99.98
1.49-1.53	0.179	95	0.1321	4554	X-RAY DIFFRACTION	100
1.53-1.57	0.152	90	0.1301	4575	X-RAY DIFFRACTION	100
1.57-1.61	0.1561	94	0.1169	4566	X-RAY DIFFRACTION	100
1.61-1.66	0.1153	90	0.1124	4560	X-RAY DIFFRACTION	100
1.66-1.71	0.1134	90	0.1087	4537	X-RAY DIFFRACTION	100
1.71-1.77	0.1067	91	0.1084	4540	X-RAY DIFFRACTION	99.98
1.77-1.84	0.1183	94	0.1045	4543	X-RAY DIFFRACTION	99.87
1.84-1.93	0.1064	147	0.1024	4489	X-RAY DIFFRACTION	99.98
1.93-2.03	0.1183	279	0.1035	4403	X-RAY DIFFRACTION	100
2.03-2.16	0.1073	281	0.097	4371	X-RAY DIFFRACTION	100
2.16-2.32	0.1102	279	0.0967	4368	X-RAY DIFFRACTION	100
2.32-2.56	0.1177	274	0.1042	4348	X-RAY DIFFRACTION	100
2.56-2.93	0.123	284	0.1058	4387	X-RAY DIFFRACTION	100
2.93-3.69	0.1206	279	0.1011	4351	X-RAY DIFFRACTION	99.91
3.69-39.39	0.093	251	0.0872	4404	X-RAY DIFFRACTION	99.94

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi