PDB-8zxt: sweet protein MNEI-Mut 6-3

ID or keywords:

Entry

Database: PDB / ID: 8zxt

Title

sweet protein MNEI-Mut 6-3

Components

Monellin chain B,Monellin chain A

Keywords

PLANT PROTEIN / a kind of food protein

Function / homology

Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / : / Monellin / Monellin / Cystatin superfamily / Monellin chain A / Monellin chain B

Function and homology information

Biological species

Dioscoreophyllum cumminsii (serendipity berry)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

You, T.J. / Liu, S.

Funding support

1items

Citation

Journal: J.Agric.Food Chem. / Year: 2025
Title: Structural Basis for the Exceptional Thermal Stability of the Boiling-Resistant Sweet Protein MNEI.
Authors: You, T. / Shi, S. / Chen, C. / Li, J. / Xu, J. / Ma, M. / Zhu, P. / Qi, T. / Dong, T. / Wang, Y. / Ye, S. / Liu, S.

History

Deposition	Jun 15, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jun 18, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jun 25, 2025	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jul 9, 2025	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8zxt.cif.gz	117.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8zxt.ent.gz	76.2 KB	Display	PDB format
PDBx/mmJSON format	8zxt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8zxt_validation.pdf.gz	433.9 KB	Display	wwPDB validaton report
Full document	8zxt_full_validation.pdf.gz	436.9 KB	Display
Data in XML	8zxt_validation.xml.gz	14.7 KB	Display
Data in CIF	8zxt_validation.cif.gz	19.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zx/8zxt ftp://data.pdbj.org/pub/pdb/validation_reports/zx/8zxt	HTTPS FTP

-
Related structure data

Related structure data	8zxjC 8zxvC 8zxyC 1iv7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#199 - Jul 2016 Monellin similarity (7)

Deposited unit

A: Monellin chain B,Monellin chain A

B: Monellin chain B,Monellin chain A

22.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Monellin chain B,Monellin chain A

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

2

B: Monellin chain B,Monellin chain A

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

Unit cell

Length a, b, c (Å)	49.627, 60.993, 65.326
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Monellin chain B,Monellin chain A / Monellin chain II / Monellin chain I Mass: 11312.838 Da / Num. of mol.: 2 / Mutation: I5E,E23A,I26R,Y65I,G83E,N90D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02882, UniProt: P02881
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.06 %
Crystal grow	Temperature: 286 K / Method: vapor diffusion, sitting drop / Details: PEG 6000 30% BIS-TRIS Propone

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.94138 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.94138 Å / Relative weight: 1
Reflection	Resolution: 1.43→27.28 Å / Num. obs: 16096 / % possible obs: 99.8 % / Redundancy: 9 % / B_iso Wilson estimate: 12.56 Å² / CC_1/2: 0.98 / Net I/σ(I): 51.9
Reflection shell	Resolution: 1.43→1.45 Å / Num. unique obs: 37657 / CC_1/2: 0.98

-
Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	model building
PHENIX	1.19_4092	refinement
HKL-3000		data reduction
PHENIX	1.19_4092	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1IV7

1iv7

Resolution: 1.9→27.28 Å / SU ML: 0.2261 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.9964
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2682	831	5.16 %
R_work	0.2229	15265	-
obs	0.2253	16096	99.75 %

Solvent computation

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

Displacement parameters

B_iso mean: 20.77 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→27.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1596	0	0	257	1853

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0034	1634
X-RAY DIFFRACTION	f_angle_d	0.6149	2196
X-RAY DIFFRACTION	f_chiral_restr	0.0451	218
X-RAY DIFFRACTION	f_plane_restr	0.0063	290
X-RAY DIFFRACTION	f_dihedral_angle_d	5.6876	218

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 (%)
1.9-2.02	0.2872	128	0.2272	2488	X-RAY DIFFRACTION	99.7
2.02-2.18	0.2921	131	0.2237	2531	X-RAY DIFFRACTION	99.92
2.18-2.4	0.3047	135	0.2271	2499	X-RAY DIFFRACTION	100
2.4-2.74	0.2556	129	0.2418	2547	X-RAY DIFFRACTION	99.89
2.74-3.45	0.2607	151	0.2189	2557	X-RAY DIFFRACTION	100
3.45-27.28	0.2524	157	0.2128	2643	X-RAY DIFFRACTION	99.04

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	4.59507975952	1.70827914209	2.00332084798	2.63791002627	-0.129794784647	3.19026754245	-0.0676860156651	-0.278357433641	0.323365258715	-0.144438193288	-0.0874439281213	0.479192833939	-0.0997974431642	-0.715303595371	0.133871461248	0.151904553189	0.00168344971912	-0.0145812311575	0.226058258327	-0.100705420243	0.302026722345	18.7686490195	61.4756037398	51.1759353888
2	2.02661894666	-1.05292165725	-2.17484773454	3.36842121177	1.76773622962	4.67427532146	-0.207017935278	-0.255576935027	-0.132343891417	0.208627738992	-0.101070272113	0.123843025285	0.331439681379	0.102782037397	0.193506174358	0.105315133376	0.00508566978374	0.0162682696432	0.118303471647	-0.024351345081	0.088653853335	32.8215194383	49.2462651557	52.9601656389
3	0.195800378296	-0.0847289631354	-0.0921712461274	0.418642799247	0.0329686721621	0.355321725527	-0.103540554048	0.0518248559588	-0.045869916549	0.0921908974186	-0.109014231526	0.14421574748	0.0777713010352	-0.1559975617	-0.549993743941	0.139032565566	-0.00752851219989	-0.00852849512406	0.132208089771	-0.21881118398	0.209749116453	23.419722995	58.2386576493	50.9609276647
4	3.13921960946	-1.04121697665	-2.22116057186	1.2049046102	1.22178668855	2.70067686216	-0.0771345521509	0.339204613312	-0.302666420029	-0.0207052438634	-0.148694323835	0.225565682872	0.173292863965	-0.278726670283	0.197950719094	0.311033717368	-0.0719679246828	0.164583902585	0.500414340979	-0.304522322084	0.530359141803	1.965237935	49.6748899499	56.5922746549
5	2.5718224829	-0.0184040402823	-1.24278043587	0.705508826619	-0.012390791407	1.39020562988	-0.0857639831244	-0.0725124589738	0.12462621022	0.095870749653	-0.102178147024	0.275250968214	0.10527473165	-0.186922976363	0.0954317197135	0.0987787252328	-0.0137874055659	-0.000353107396534	0.176848639025	-0.0948061021055	0.170642700596	25.365789366	53.2997710522	49.8560477013
6	2.55179951462	-0.055247712286	-1.37780209167	1.35542380184	-0.160121988363	2.41040573368	-0.0497268387662	-0.125846404376	-0.115470133775	0.152218025658	-0.207806120863	0.288248445043	-0.0342433916542	-0.177688700563	0.102223661992	0.119455313324	-0.0187935398062	0.0243265769448	0.223791616389	-0.0648751924218	0.153641347234	24.0714377503	50.2829668937	51.1053221625
7	2.20592609921	-2.42230964838	1.99016136285	6.9314542535	-2.86978192389	7.71129371433	-0.0796069170041	0.309460904601	0.392413392039	0.0638450938158	-0.0822244772127	-0.469263709656	-0.00453618240282	0.759549154023	0.200043665094	0.139628627046	-0.0725895450033	0.0189016346681	0.153630469039	0.0347826694943	0.183214680291	30.5494945198	62.8291868134	29.7394375297
8	4.15875643808	2.43190897484	-0.713195194362	8.2774790004	-0.320623823288	1.92705712274	-0.111959881335	0.276423065995	0.0548146769168	-0.341533890469	-0.197368201066	-0.196961333144	-0.078642307115	0.122836461127	0.269669521965	0.0838931833794	-0.0159835439636	-0.0222567394309	0.148229062	0.00935143517291	0.0795715368471	18.6637635077	52.4633531938	24.240188083
9	1.89036035716	0.276054739503	0.174006327371	4.87320196981	0.667088780107	0.674493989825	0.186929973929	-0.153542927981	-0.0610305591125	0.184425416052	-0.091470819677	0.104060465729	0.287864900859	-0.0541499348907	0.0413215674057	0.184482911557	-0.103255940303	-0.0271175344788	0.19477923339	-0.00554402840592	0.108057260484	11.0779700246	46.9504761578	31.0364300811
10	0.443905210343	0.026460444878	0.0915278292838	0.262483493014	-0.141517680875	0.16870452381	-0.06474450848	-0.00301160132209	0.0789480715362	0.0445124668056	-0.00840848264092	-0.0363965130278	-0.10363930043	-0.000783548351323	-0.122431248934	0.124512419544	-0.000768805800587	-0.0677696174302	0.0540852223012	0.0931054760093	0.188135317128	26.0340207193	59.8541175077	29.3290773749
11	0.663276717426	0.0123403571179	-0.499348057018	0.851518433298	0.376045031844	0.870285866296	-0.0557031624482	-0.146846033505	-0.142463743895	0.189613140025	0.109619301808	0.0845952931484	0.104212107958	-0.0641617464564	-0.115050975004	0.193310954022	0.0539406568818	0.0113301717622	0.346014473596	0.289311920155	0.424833470645	47.8761798174	51.6817218589	24.3082210197
12	4.19886916804	0.324808404073	-1.48716092643	0.640733919182	-0.457695740642	1.53263494707	-0.0342067785089	-0.0168762040502	0.0708654235565	0.0106690275734	-0.0488877243516	-0.0759910184805	0.218106081431	0.15767373811	0.134281940976	0.0624499199742	-0.0278739056761	-0.0551085980801	0.157641088805	0.0290837846966	0.0773917942386	27.3927283663	55.6163014072	28.6115243928
13	3.88317124575	-1.14495929627	-0.602866666279	0.98232036145	0.678189969157	1.74301757083	-0.109023868227	0.0755037888619	0.0816773706812	-0.0172995315753	0.0115149604343	0.0562736565408	-0.0039638850779	0.0163052611393	-0.0324068396486	0.0580620858908	-0.0351456214919	-0.0578473800365	0.117640781273	0.0628970622979	0.117203767282	20.5055213064	53.4239720488	31.1133710062
14	5.36791810595	2.14090441674	-0.435767684364	3.13627266112	0.7302132759	0.989183745291	-0.509078148249	0.852855976917	0.0400804061681	-0.527573392452	0.503241770604	0.672674770237	0.367806118427	-0.476069094454	0.0534395865495	0.386793769596	-0.262071460464	0.0665993865336	0.381670939432	-0.0261706147255	0.37640572248	33.1657726494	50.3504336484	16.3459476676
15	5.12231717253	-1.14921851414	-2.26436656868	2.75104848946	2.1691863354	4.15621026487	-0.0270359656723	-0.330455370274	0.0981018834399	0.0794203120133	0.12626948352	-0.112836782049	0.0349662863217	-0.0587891371893	-0.106677564308	0.0830509136665	-0.0577353166497	-0.00812157516594	0.134943044946	0.0215751735729	0.120405299343	21.6137182884	51.8702666863	33.8632330522

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 'A' and (resid 1 through 9 )	A	A	1 - 9	1 - 9
2	2	chain 'A' and (resid 10 through 33 )	A	A	10 - 33	10 - 33
3	3	chain 'A' and (resid 34 through 47 )	A	A	34 - 47	34 - 47
4	4	chain 'A' and (resid 48 through 54 )	A	A	48 - 54	48 - 54
5	5	chain 'A' and (resid 55 through 78 )	A	A	55 - 78	55 - 78
6	6	chain 'A' and (resid 79 through 96 )	A	A	79 - 96	79 - 96
7	7	chain 'B' and (resid 1 through 9 )	B	B	1 - 9	1 - 9
8	8	chain 'B' and (resid 10 through 26 )	B	B	10 - 26	10 - 26
9	9	chain 'B' and (resid 27 through 33 )	B	B	27 - 33	27 - 33
10	10	chain 'B' and (resid 34 through 47 )	B	B	34 - 47	34 - 47
11	11	chain 'B' and (resid 48 through 54 )	B	B	48 - 54	48 - 54
12	12	chain 'B' and (resid 55 through 66 )	B	B	55 - 66	55 - 66
13	13	chain 'B' and (resid 67 through 78 )	B	B	67 - 78	67 - 78
14	14	chain 'B' and (resid 79 through 83 )	B	B	79 - 83	79 - 83
15	15	chain 'B' and (resid 84 through 96 )	B	B	84 - 96	84 - 96

-
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