PDB-7odj: Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocycl...

ID or keywords:

Entry

Database: PDB / ID: 7odj

Title

Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocyclophellitol aziridine

Components

Man5A

Keywords

HYDROLASE / Mannosidase / covalent inhibitor / cyclophellitol / cellvibrio

Function / homology

Mannan endo-1,4-beta-mannosidase-like / mannan endo-1,4-beta-mannosidase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / ACETATE ION / Chem-VEE / Man5A

Function and homology information

Biological species

Cellvibrio mixtus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 Å

Authors

McGregor, N.G.S. / Davies, G.J.

Funding support

United Kingdom, 2items

Citation

Journal: Org.Biomol.Chem. / Year: 2022
Title: Synthesis of broad-specificity activity-based probes for exo -beta-mannosidases.
Authors: McGregor, N.G.S. / Kuo, C.L. / Beenakker, T.J.M. / Wong, C.S. / Offen, W.A. / Armstrong, Z. / Florea, B.I. / Codee, J.D.C. / Overkleeft, H.S. / Aerts, J.M.F.G. / Davies, G.J.

History

Deposition	Apr 29, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7odj.cif.gz	329.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7odj.ent.gz		Display	PDB format
PDBx/mmJSON format	7odj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7odj_validation.pdf.gz	719.6 KB	Display	wwPDB validaton report
Full document	7odj_full_validation.pdf.gz	721.4 KB	Display
Data in XML	7odj_validation.xml.gz	20.9 KB	Display
Data in CIF	7odj_validation.cif.gz	32.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/od/7odj ftp://data.pdbj.org/pub/pdb/validation_reports/od/7odj	HTTPS FTP

-
Related structure data

Related structure data	7omiC 7omsC 7op6C 7op7C 1uuqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1uuq-d 1uz4-d 3gt5-d 3ckz-d 7s43-1 2ibo-d 1jdw-d 2htw-d 6sud-1 7jdw-d Search similar-shape structures by Omokage search (details) 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

AAA: Man5A

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	91.815, 102.230, 50.680
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Man5A Mass: 50230.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellvibrio mixtus (bacteria) / Gene: man5A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6QT42
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-VEE / (1R,2S,3R,4S,5R,6R)-5-(8-azidooctylamino)-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol / N-alkyl mannocyclophellitol aziridine Mass: 330.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₃₀N₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.05 % / Description: Rods
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.2 M ammonium sulfate, 24% PEG4000

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.97629 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 24, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97629 Å / Relative weight: 1

Reflection

Resolution: 1.3→68.403 Å / Num. obs: 116329 / % possible obs: 98.8 % / Redundancy: 21.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.116 / R_pim(I) all: 0.035 / R_rim(I) all: 0.121 / Net I/σ(I): 21.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
7.12-68.31	24.4	0.041	844	0.999	0.011	0.043	99.8
1.3-1.32	4.8	0.8	4839	0.631	0.586	0.998	84.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
REFMAC	5.8.0267	refinement
Aimless	0.7.4	data scaling
MOLREP		phasing
Coot		model building
REFMAC	5.8.0267	refinement
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1UUQ

1uuq

Resolution: 1.3→68.403 Å / Cor.coef. F_o:F_c: 0.98 / Cor.coef. F_o:F_c free: 0.958 / SU B: 1.357 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1577	5818	5.004 %
R_work	0.1246	110442	-
all	0.126	-	-
obs	-	116260	98.636 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 15.895 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.399 Å²	0 Å²	-0 Å²
2-	-	0.962 Å²	0 Å²
3-	-	-	0.436 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→68.403 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3292	0	44	424	3760

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	3626
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	3272
X-RAY DIFFRACTION	r_angle_refined_deg	1.917	1.642	4968
X-RAY DIFFRACTION	r_angle_other_deg	1.623	1.58	7558
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.245	5	464
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.852	23.255	212
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.442	15	596
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.457	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.117	0.2	456
X-RAY DIFFRACTION	r_chiral_restr_other	0.075	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	4224
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	904
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	776
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	3122
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	1751
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.088	0.2	1565
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	288
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.226	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.265	0.2	31
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.089	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	2.075	1.433	1700
X-RAY DIFFRACTION	r_mcbond_other	1.848	1.43	1698
X-RAY DIFFRACTION	r_mcangle_it	2.293	2.159	2138
X-RAY DIFFRACTION	r_mcangle_other	2.301	2.163	2139
X-RAY DIFFRACTION	r_scbond_it	3.427	1.699	1926
X-RAY DIFFRACTION	r_scbond_other	3.426	1.699	1927
X-RAY DIFFRACTION	r_scangle_it	3.918	2.468	2803
X-RAY DIFFRACTION	r_scangle_other	3.917	2.468	2804
X-RAY DIFFRACTION	r_lrange_it	3.57	17.938	4415
X-RAY DIFFRACTION	r_lrange_other	3.436	17.318	4311
X-RAY DIFFRACTION	r_rigid_bond_restr	4.168	3	6896

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 (%)
1.3-1.334	0.26	379	0.234	6972	X-RAY DIFFRACTION	84.8453
1.334-1.37	0.221	386	0.196	7731	X-RAY DIFFRACTION	96.9773
1.37-1.41	0.201	412	0.158	7794	X-RAY DIFFRACTION	100
1.41-1.453	0.166	404	0.121	7510	X-RAY DIFFRACTION	100
1.453-1.501	0.144	391	0.099	7322	X-RAY DIFFRACTION	100
1.501-1.554	0.138	371	0.092	7084	X-RAY DIFFRACTION	100
1.554-1.612	0.133	355	0.083	6848	X-RAY DIFFRACTION	100
1.612-1.678	0.143	353	0.082	6609	X-RAY DIFFRACTION	100
1.678-1.753	0.117	312	0.081	6346	X-RAY DIFFRACTION	100
1.753-1.838	0.13	339	0.085	6035	X-RAY DIFFRACTION	100
1.838-1.938	0.148	320	0.099	5759	X-RAY DIFFRACTION	100
1.938-2.055	0.154	291	0.119	5479	X-RAY DIFFRACTION	100
2.055-2.197	0.165	272	0.118	5153	X-RAY DIFFRACTION	100
2.197-2.373	0.138	250	0.108	4817	X-RAY DIFFRACTION	100
2.373-2.599	0.135	210	0.107	4458	X-RAY DIFFRACTION	100
2.599-2.906	0.143	224	0.122	4035	X-RAY DIFFRACTION	100
2.906-3.355	0.163	194	0.145	3596	X-RAY DIFFRACTION	100
3.355-4.108	0.159	156	0.145	3062	X-RAY DIFFRACTION	100
4.108-5.805	0.164	124	0.137	2417	X-RAY DIFFRACTION	100
5.805-68.403	0.241	75	0.203	1416	X-RAY DIFFRACTION	99.866

-
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