PDB-7tsw: Crystal Structure Of Human NADH-Cytochrome B5 Reductase T117D Mutant

ID or keywords:

Entry

Database: PDB / ID: 7tsw

Title

Crystal Structure Of Human NADH-Cytochrome B5 Reductase T117D Mutant

Components

NADH-cytochrome b5 reductase 3

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

nitric-oxide synthase complex / cytochrome-b5 reductase / Vitamin C (ascorbate) metabolism / cytochrome-b5 reductase activity, acting on NAD(P)H / Phase I - Functionalization of compounds / blood circulation / cholesterol biosynthetic process / AMP binding / hemoglobin complex / nitric oxide biosynthetic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Zheng, A. / Thibodeau, P.H.

Funding support

United States, 1items

Citation

Journal: To be published
Title: Structure Of wild-type Human NADH-Cytochrome B5 Reductase and mutants
Authors: Zheng, A. / Thibodeau, P.H.

History

Deposition	Jan 31, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 8, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7tsw.cif.gz	790.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7tsw.ent.gz	555.3 KB	Display	PDB format
PDBx/mmJSON format	7tsw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7tsw_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	7tsw_full_validation.pdf.gz	2.3 MB	Display
Data in XML	7tsw_validation.xml.gz	60.6 KB	Display
Data in CIF	7tsw_validation.cif.gz	82.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ts/7tsw ftp://data.pdbj.org/pub/pdb/validation_reports/ts/7tsw	HTTPS FTP

-
Related structure data

Related structure data	7thgC 7tnvC 1umkS C: citing same article (ref.) S: Starting model for refinement
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	#208 - Apr 2017 Glucose Transporters similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #133 - Jan 2011 Nitric Oxide Synthase similarity (3) #228 - Dec 2018 Directed Evolution of Enzymes similarity (3)

Deposited unit

A: NADH-cytochrome b5 reductase 3

B: NADH-cytochrome b5 reductase 3

C: NADH-cytochrome b5 reductase 3

D: NADH-cytochrome b5 reductase 3

E: NADH-cytochrome b5 reductase 3

F: NADH-cytochrome b5 reductase 3

hetero molecules

192 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NADH-cytochrome b5 reductase 3

hetero molecules

defined by author
Evidence: gel filtration
32 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: NADH-cytochrome b5 reductase 3

hetero molecules

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

3

C: NADH-cytochrome b5 reductase 3

hetero molecules

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

4

D: NADH-cytochrome b5 reductase 3

hetero molecules

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

5

E: NADH-cytochrome b5 reductase 3

hetero molecules

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

6

F: NADH-cytochrome b5 reductase 3

hetero molecules

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

Unit cell

Length a, b, c (Å)	162.562, 79.986, 172.358
Angle α, β, γ (deg.)	90.000, 98.672, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	NADH-cytochrome b5 reductase 3 Mass: 31165.955 Da / Num. of mol.: 6 / Mutation: T117D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYB5R3, DIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00387
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.01 Å³/Da / Density % sol: 59.19 %
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: PEG 4K 10%, 0.1M Tris-HCl pH 8.4

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
Detector	Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 27, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 2.4→46.03 Å / Num. obs: 80627 / % possible obs: 94 % / Redundancy: 7.71 % / B_iso Wilson estimate: 51.6 Å² / R_merge(I) obs: 0.111 / R_rim(I) all: 0.12 / Net I/σ(I): 8.7
Reflection shell	Resolution: 2.4→2.49 Å / Redundancy: 8.62 % / R_merge(I) obs: 0.471 / Mean I/σ(I) obs: 3 / Num. unique obs: 7363 / R_rim(I) all: 0.5 / % possible all: 86.8

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
Coot		model building
PHENIX		phasing
d*TREK		data reduction
d*TREK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1umk

1umk

Resolution: 2.4→38.66 Å / SU ML: 0.3781 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.8546
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2641	1999	2.48 %
R_work	0.2266	78547	-
obs	0.2276	80546	93.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 64.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→38.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12918	0	318	320	13556

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0073	13621
X-RAY DIFFRACTION	f_angle_d	0.9957	18551
X-RAY DIFFRACTION	f_chiral_restr	0.0584	1994
X-RAY DIFFRACTION	f_plane_restr	0.0084	2371
X-RAY DIFFRACTION	f_dihedral_angle_d	22.8224	5125

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 (%)
2.4-2.46	0.3792	130	0.3204	5122	X-RAY DIFFRACTION	86.5
2.46-2.53	0.344	133	0.3027	5208	X-RAY DIFFRACTION	87.44
2.53-2.6	0.3634	132	0.3099	5205	X-RAY DIFFRACTION	87.64
2.6-2.68	0.3707	134	0.3083	5271	X-RAY DIFFRACTION	88.91
2.68-2.78	0.3623	137	0.3128	5342	X-RAY DIFFRACTION	89.94
2.78-2.89	0.3685	138	0.3059	5426	X-RAY DIFFRACTION	91.26
2.89-3.02	0.3563	142	0.3022	5580	X-RAY DIFFRACTION	93.25
3.02-3.18	0.3197	143	0.3018	5676	X-RAY DIFFRACTION	95.74
3.18-3.38	0.3292	147	0.276	5802	X-RAY DIFFRACTION	96.86
3.38-3.64	0.2796	151	0.2331	5876	X-RAY DIFFRACTION	98.43
3.64-4.01	0.2408	150	0.2111	5932	X-RAY DIFFRACTION	99.35
4.01-4.59	0.2277	152	0.1761	5976	X-RAY DIFFRACTION	99.64
4.59-5.78	0.2004	154	0.1784	6033	X-RAY DIFFRACTION	99.95
5.78-38.66	0.2033	156	0.1799	6098	X-RAY DIFFRACTION	99.14

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.95571059321	2.03539636058	-0.958687996398	4.40324698988	1.34605095185	1.71762621924	-0.529820222311	1.85034058466	0.339091201209	-1.17792643523	0.756698045594	0.0470402498408	-0.278800201723	0.0363417121642	-0.202805853318	0.76131296834	-0.312815193225	-0.111557464084	1.50161577288	0.160099369133	0.559801759448	-69.7789650946	-60.2809717966	46.3200738657
2	7.25680226627	3.18257764115	0.89025398276	4.23254409642	0.645100088432	2.5290860552	-0.0232012203436	-0.974513238981	-0.281968242599	-0.170386173211	-0.35262126943	-0.0936037307845	-0.0302302522748	0.0138883151364	0.375729381346	0.304076779489	0.0760117438494	0.030603363931	0.432261530869	0.0437677907739	0.482289318585	-7.2924676567	-32.2678060236	20.6582292363
3	2.49999132081	-0.090290605096	-0.200094777626	4.22121236097	1.68516765197	3.52050853714	0.13294906855	-1.11463354091	0.170995103443	0.784279267083	-0.432836154213	0.735667498588	-0.20258098832	-0.312037084296	0.260048311973	0.591830518371	-0.164243905377	0.141480394645	1.04976434292	-0.152068351991	0.72166877119	-15.0585711324	-23.91867113	39.2397274682
4	2.78599023444	-0.569966212671	-0.395706979207	4.95419928222	0.0188401031399	2.82093112299	-0.00337142633156	0.180830264535	0.24483747896	-0.33070643534	-0.00222955796328	-0.709963615029	-0.0240089220943	0.222117155966	0.0142357025462	0.356471222912	0.0191693457377	0.0593913863299	0.251365087227	0.0273422784227	0.409692952512	-29.018231733	-18.1196385831	-12.2143030822
5	3.2113914279	-1.19913214434	0.0248412224647	5.03764563905	0.243991227051	2.59418337435	-0.0369585921015	0.0836808981076	0.211476598647	-0.236909431782	0.036994753595	0.0304844130485	-0.205766245647	-0.192859040516	0.0310576607122	0.410852700491	0.0260802770977	0.00976969154208	0.278258580565	0.0072211561953	0.317603155695	-39.5214098629	-13.9352303145	-10.7175750785
6	3.7578024494	-0.568595836435	-0.0607409898511	3.21727165918	-0.565167986916	1.96013178006	-0.0239701612425	-0.00246316706408	0.24417504025	0.306644394412	0.0553473797305	-0.574986709697	-0.0907148395838	0.297486237801	-0.0187157138093	0.363833677186	-0.0050596530052	-0.0792185717641	0.295712810666	-0.0516455935459	0.380280396748	-28.0360788954	-22.5294900979	7.72677882234
7	3.95911110521	-0.544886640159	-0.114970441802	4.58190678407	-0.0476837682656	1.84416622913	-0.0708162531245	-0.206995614079	-0.0574048337939	0.236945388303	0.140590566228	0.135963985502	0.137742105134	-0.122442772284	-0.058629805499	0.383812226639	0.00932769902001	-0.035347406415	0.275867705524	0.00975448632382	0.284677121999	-41.5670754329	-27.0598519177	10.6942726708
8	3.84315653102	-0.642220872617	1.64844570707	5.00913792868	0.0710666584007	4.38763476362	0.238801646484	0.108817512995	-0.142231349261	-0.656524023379	-0.169084327947	0.576648570664	0.200027326537	-0.566758890719	-0.0635616014411	0.591793511939	0.048377786876	-0.0563164455477	0.453358139593	-0.0559682102578	0.455440909222	-72.9292234277	-28.9922041166	70.8911781814
9	2.35559164484	0.288714174398	0.340817950788	4.13657228243	-0.203389677989	2.23299377119	0.0533930496402	-0.3422275482	-0.103721808875	0.583719005418	-0.0928648134943	0.267710003336	0.0317795607841	-0.155966699572	0.0469425690203	0.432660239681	0.0171563039329	0.0536697909451	0.387462396301	-0.0457068342134	0.382939245243	-66.5161348827	-36.1686574223	90.3335328358
10	3.67622980243	1.08577851361	1.48354934387	1.86170068907	0.901704521275	3.33494636846	-0.267838787442	1.11685289508	0.216780032811	-0.366007476052	0.196294197818	-0.05084396799	-0.0181043869291	0.316720957378	0.0838004843649	0.408160846643	-0.0649357147274	0.0632932329006	0.641944505664	0.0919951084443	0.370251261696	-38.6037764652	-43.617589203	56.7117381886
11	3.27145964121	-0.0230002125211	0.0716043139075	3.89814813161	0.430778275177	2.12535734884	-0.125730272902	0.271551477312	-0.100793006948	0.0127104047093	0.0573250481126	-0.335358214332	0.142567411109	0.434504048977	0.0853896936121	0.375091276359	0.0383615448233	0.0371129006432	0.499906365499	0.0388769513358	0.359753754625	-24.0504152177	-49.2596285324	70.692154495
12	4.4084104753	0.918523454146	-0.71764100506	4.10111725869	-2.80231377612	6.60945836563	0.575046097986	-1.34164217031	-0.316568189629	1.19653813035	-0.51711551756	-0.0889345885511	-0.0630505850432	0.664848144628	-0.0658928967645	0.758787446386	-0.0819092882493	-0.0190975656834	0.745721070805	0.0362131810715	0.406319658366	-48.6985118136	-10.4268719876	39.2100886494
13	4.96960223601	1.67208177597	-1.23323031249	4.94396940236	-1.9131963667	3.78371631348	0.232370432884	0.0253940954058	0.183382831565	0.0183568093638	0.236075896186	0.815542689047	-0.0604381873852	-0.313581858581	-0.435587520205	0.356682327836	0.0545599810531	0.03328700337	0.284270792274	0.049800157162	0.435472210348	-59.6536513674	-4.08386413568	20.8872507102
14	3.48648418706	1.78104376215	-0.553562736189	3.59688277401	-0.539423434369	4.16932517436	-0.159907869788	0.499784420337	-0.24738531003	-0.351791680189	0.165730156935	-0.0224455086444	0.00314377253203	-0.356141817176	0.00890842873925	0.385498395111	-0.0368184452505	0.0163245884729	0.435908510034	-0.06784459627	0.352232899495	-71.5661278921	-73.1885797628	68.3211771072
15	6.7806110188	0.14073249137	-2.16101420683	3.84648701675	0.240144216149	3.0551345091	-0.685706507177	1.31354962833	-0.813008721931	-0.716162343207	0.46177908904	-0.5083028483	0.32880540339	0.0640832279418	0.174587404431	0.537583724041	-0.152669069321	0.0934675989118	0.669774132957	-0.204614188483	0.456134517193	-60.6551555491	-67.196307608	55.7586780873
16	4.32862412682	0.87512966849	-0.700068099345	5.31553996962	-1.19068979404	2.08969112408	-0.0389225389379	0.499181615482	0.224553517916	0.213611420322	0.140102995048	0.0449045555775	-0.0219664450005	-0.000972155905523	-0.0749721552651	0.412334505067	-0.0790768051061	0.0111696751872	0.516279719662	-0.050674453115	0.30817229852	-59.0578028044	-54.4452038944	59.0646506731

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'E' and (resid 255 through 301 )	E	I	255 - 301	217 - 263
2	2	chain 'F' and (resid 31 through 138 )	F	K	31 - 138	1 - 108
3	3	chain 'F' and (resid 139 through 301 )	F	K	139 - 301	109 - 271
4	4	chain 'A' and (resid 31 through 78 )	A	A	31 - 78	1 - 48
5	5	chain 'A' and (resid 79 through 143 )	A	A	79 - 143	49 - 113
6	6	chain 'A' and (resid 144 through 210 )	A	A	144 - 210	114 - 180
7	7	chain 'A' and (resid 211 through 301 )	A	A	211 - 301	181 - 271
8	8	chain 'B' and (resid 31 through 138 )	B	C	31 - 138	1 - 108
9	9	chain 'B' and (resid 139 through 301 )	B	C	139 - 301	109 - 271
10	10	chain 'C' and (resid 31 through 173 )	C	E	31 - 173	1 - 143
11	11	chain 'C' and (resid 174 through 301 )	C	E	174 - 301	144 - 271
12	12	chain 'D' and (resid 32 through 153 )	D	G	32 - 153	1 - 122
13	13	chain 'D' and (resid 154 through 301 )	D	G	154 - 301	123 - 270
14	14	chain 'E' and (resid 31 through 173 )	E	I	31 - 173	1 - 135
15	15	chain 'E' and (resid 174 through 210 )	E	I	174 - 210	136 - 172
16	16	chain 'E' and (resid 211 through 254 )	E	I	211 - 254	173 - 216

-
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