PDB-6mnj: Hadza microbial sialidase Hz136

ID or keywords:

Entry

Database: PDB / ID: 6mnj

Title

Hadza microbial sialidase Hz136

Components

Hz136

Keywords

HYDROLASE / Sialidase / microbiome / Hadza / Neu5Gc / Neu5Ac / sialic acid / inflammation / season

Function / homology

Function and homology information

exo-alpha-sialidase activity
Similarity search - Function

Biological species

Alistipes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Rees, S.D. / Zaramela, L. / Zengler, K. / Chang, G.

Funding support

United States, 1items

Citation

Journal: Nat Microbiol / Year: 2019
Title: Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates.
Authors: Zaramela, L.S. / Martino, C. / Alisson-Silva, F. / Rees, S.D. / Diaz, S.L. / Chuzel, L. / Ganatra, M.B. / Taron, C.H. / Secrest, P. / Zuniga, C. / Huang, J. / Siegel, D. / Chang, G. / Varki, A. / Zengler, K.

#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.

#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...

History

Deposition	Oct 1, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 2, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 11, 2019	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6mnj.cif.gz	682.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6mnj.ent.gz	474 KB	Display	PDB format
PDBx/mmJSON format	6mnj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6mnj_validation.pdf.gz	437.1 KB	Display	wwPDB validaton report
Full document	6mnj_full_validation.pdf.gz	442.1 KB	Display
Data in XML	6mnj_validation.xml.gz	35 KB	Display
Data in CIF	6mnj_validation.cif.gz	48.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mn/6mnj ftp://data.pdbj.org/pub/pdb/validation_reports/mn/6mnj	HTTPS FTP

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Related structure data

Related structure data	6mrvC 6mrxC 6myvC 4q6kS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3wdm-2 3bip-1 5oa2-3 3e90-d 3gdr-1 3wdl-2 3cb6-d 3pf9-1 3gdk-1 1fwn-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#113 - May 2009 Influenza Neuraminidase similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (1)

Deposited unit

A: Hz136

B: Hz136

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

1

A: Hz136

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

2

B: Hz136

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	119.670, 145.395, 150.290
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222
Space group name Hall	I22
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z #4: -x,-y,z #5: x+1/2,y+1/2,z+1/2 #6: x+1/2,-y+1/2,-z+1/2 #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

#1: Protein	Hz136 Mass: 61261.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alistipes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: R6X4Z0*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.36 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 0.1 M Bis Tris Propane, 0.2 M Sodium Citrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99994 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99994 Å / Relative weight: 1
Reflection	Resolution: 2.2→75.14 Å / Num. obs: 128523 / % possible obs: 100 % / Redundancy: 12.7 % / B_iso Wilson estimate: 19.57 Å² / Net I/σ(I): 10.5
Reflection shell	Resolution: 2.2→2.25 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
BOS		data collection
MOSFLM		data reduction
PHENIX		phasing
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4Q6K

4q6k

Resolution: 2.2→72.7 Å / SU ML: 0.2614 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 26.2776

	R_factor	Num. reflection	% reflection
R_free	0.2387	6451	5.02 %
R_work	0.2135	-	-
obs	0.2148	128523	99.91 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 30.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→72.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7954	0	0	142	8096

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0023	8124
X-RAY DIFFRACTION	f_angle_d	0.5931	11038
X-RAY DIFFRACTION	f_chiral_restr	0.0478	1238
X-RAY DIFFRACTION	f_plane_restr	0.0033	1432
X-RAY DIFFRACTION	f_dihedral_angle_d	12.4233	4868

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 (%)
2.2-2.23	0.3434	206	0.2944	4095	X-RAY DIFFRACTION	99.98
2.23-2.25	0.4401	173	0.3928	4049	X-RAY DIFFRACTION	98.97
2.25-2.28	0.3593	221	0.3228	4104	X-RAY DIFFRACTION	99.65
2.28-2.31	0.3174	177	0.2706	4086	X-RAY DIFFRACTION	100
2.31-2.34	0.2901	188	0.2588	4054	X-RAY DIFFRACTION	99.98
2.34-2.37	0.2711	232	0.2513	4082	X-RAY DIFFRACTION	99.95
2.37-2.4	0.3023	186	0.2576	4130	X-RAY DIFFRACTION	99.95
2.4-2.44	0.323	213	0.2622	4047	X-RAY DIFFRACTION	99.93
2.44-2.48	0.2793	262	0.246	4031	X-RAY DIFFRACTION	99.98
2.48-2.52	0.2339	165	0.248	4119	X-RAY DIFFRACTION	100
2.52-2.56	0.2771	212	0.2432	4120	X-RAY DIFFRACTION	100
2.56-2.61	0.3139	196	0.2569	4003	X-RAY DIFFRACTION	100
2.61-2.66	0.3064	216	0.2707	4073	X-RAY DIFFRACTION	99.88
2.66-2.71	0.3491	207	0.2622	4080	X-RAY DIFFRACTION	99.91
2.71-2.77	0.2845	190	0.2562	4111	X-RAY DIFFRACTION	99.91
2.77-2.84	0.2382	206	0.2428	4087	X-RAY DIFFRACTION	99.95
2.84-2.91	0.2649	228	0.2357	4053	X-RAY DIFFRACTION	100
2.91-2.99	0.2755	233	0.2396	4038	X-RAY DIFFRACTION	100
2.99-3.07	0.2798	241	0.2377	4065	X-RAY DIFFRACTION	100
3.07-3.17	0.268	178	0.2255	4148	X-RAY DIFFRACTION	100
3.17-3.29	0.2556	228	0.2273	4001	X-RAY DIFFRACTION	100
3.29-3.42	0.2617	212	0.2088	4090	X-RAY DIFFRACTION	100
3.42-3.57	0.2382	223	0.2039	4056	X-RAY DIFFRACTION	99.95
3.57-3.76	0.2233	251	0.1866	4081	X-RAY DIFFRACTION	99.91
3.76-4	0.1743	187	0.1801	4073	X-RAY DIFFRACTION	99.88
4-4.31	0.1872	211	0.142	4091	X-RAY DIFFRACTION	100
4.31-4.74	0.147	311	0.1292	3918	X-RAY DIFFRACTION	100
4.74-5.42	0.1393	219	0.1238	4091	X-RAY DIFFRACTION	100
5.42-6.83	0.1799	212	0.1582	4074	X-RAY DIFFRACTION	100
6.83-72.74	0.1822	267	0.172	4022	X-RAY DIFFRACTION	99.58

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	0.801431503188	0.338841311571	-0.158133747158	0.491218889422	-0.162820507791	0.779629555299	0.0565160184592	-0.280255960085	0.0331315485334	0.105577488499	-0.0802752102039	-0.0457231874488	-0.0200286063982	0.0144904752419	0.00780732106759	0.183089497699	-0.0155748127835	-0.033474608459	0.215667996048	0.0261859522661	0.131950353139	-12.9802023514	23.5352213474	63.104327229
2	0.754988405606	0.165912914491	-0.160617538346	0.274633637275	-0.101071562393	0.541047734409	0.0382860827949	0.0515669339422	-0.0200184446571	0.0262371265639	0.0190046902287	-0.0146271799745	0.028149174084	0.0257040634661	-0.0450927032508	0.162217492465	0.00711869531352	0.00308776322499	0.139322035612	0.0188249523879	0.244213936578	-6.22923076024	32.6669029516	35.9534702095
3	0.657372483049	0.0793646877818	0.109646340236	0.433298947563	0.201982563135	0.573200897938	0.0239182093779	0.0421329746373	-0.0299653918686	0.0221488660704	0.0375511520951	-0.137107722388	-0.0124751557356	0.0423005056534	-0.0600067998254	0.17125660152	-0.00230575455823	0.0126129621581	0.156234346151	-0.00175190372453	0.28212129761	9.48433365579	30.1065421143	33.9250733072
4	0.693411903435	0.19533760703	-0.420719027167	0.912159666897	-0.0807716669368	1.15347194474	-0.0429974424687	0.218229655002	-0.128482036422	-0.0140416941109	0.116465633235	0.0478691377889	0.00860536735859	-0.000763339697467	-0.0495646691765	0.164819801165	-0.0352246151597	-0.0411902130795	0.259093533134	-0.0125814748529	0.144940961153	-31.4355572462	19.0196551543	12.1202940462
5	1.39831370272	0.0888490380825	-0.0454122881711	1.00656261031	0.0688702424935	1.27293040261	0.0603545903849	0.131611722947	-0.245753827165	-0.126755799796	0.0829425284586	-0.17617571592	-0.00951255992931	0.236826084849	-0.0625687446068	0.141756899987	-0.00235152110822	-0.0204388539412	0.180961424575	-0.0349948230825	0.211423484619	-21.731734442	20.2287199902	20.8689396209
6	0.60915453684	0.0842391819968	0.0826964006036	0.653550447146	-0.362070985464	0.721493397083	0.101697057048	0.292167399208	0.120612042905	-0.058135464071	0.0247649411924	0.0132896687151	-0.0992658031238	-0.0248201620315	-0.0988240852672	0.186026988282	0.00913181172304	-0.012379655005	0.244547433444	-0.0192008045076	0.221552139153	-32.7763805682	22.7625356227	12.5100255652
7	0.589643840639	0.101478609602	0.139409603975	0.828448186202	-0.402909592786	0.273037767735	-0.0603212617965	0.175391644466	-0.106084862653	-0.113188987768	0.0622221318078	0.0344166077987	0.200651489327	0.101730795022	-0.0140555377019	0.175293731484	-0.0054524098389	-0.0407429079499	0.180797691781	0.00451046197264	0.192705026169	-34.3492061667	14.4876424903	20.8231547846
8	1.50591044266	-0.00549801927325	0.376768071757	0.436699109478	-0.0920122600585	0.747384373058	0.123599573082	-0.0634828190532	-0.247896341602	0.0965619946367	-0.0117712332241	0.0961329091167	0.0452315995301	0.098022755801	-0.0784835159811	0.154217245932	0.00319169119237	-0.00258109632275	0.110743545271	0.0156229791504	0.208980828778	-36.8122574905	11.8761403926	46.668615669
9	0.73067387978	-0.00767943166728	-0.110417689719	1.07705902088	0.0320136859949	0.671552535096	0.0448392448338	-0.0714435750784	-0.0439688856666	0.299051836099	-0.0314742271497	0.0403199543532	-0.0247278084838	-0.00151386906625	-0.0426645340867	0.242477690719	-0.000361153888717	0.0175378766407	0.197881370294	0.0633165027249	0.277169768887	-36.3179584146	0.916722406937	54.4394447684
10	0.713059338541	-0.0317771647252	0.0900331329419	0.912468095134	0.131960001993	0.778077311832	-0.0346766533883	-0.00846588747086	-0.171388128045	0.0512223149758	-0.0329140795541	0.137649339171	0.0676028528217	-0.0334130301567	0.10589046748	0.20201607756	0.00703139092562	0.0022169816245	0.168584221539	0.0431216488956	0.367467287315	-37.3777363988	-11.5322417731	42.6784902679
11	0.447431313706	-0.0527530888744	0.199734560765	0.830526066168	0.021046039199	0.657637584493	-0.0234831698943	0.106337161008	-0.193500526468	-0.19458278768	0.0205184821678	0.220729851082	0.0768107814302	-0.0120071182622	-0.0540912097078	0.179775549922	-0.00515572055593	-0.0287593162114	0.15145105127	-0.00307552921089	0.296453843654	-39.9991806778	-0.594526721384	27.6174942922

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 166 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 167 through 299 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 300 through 538 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 24 through 79 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 80 through 120 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 121 through 156 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 157 through 207 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 208 through 270 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 271 through 344 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 345 through 453 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 454 through 538 )

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