PDB-6z1m: Structure of an Ancestral glycosidase (family 1) bound to heme

ID or keywords:

Entry

Database: PDB / ID: 6z1m

Title

Structure of an Ancestral glycosidase (family 1) bound to heme

Components

Ancestral reconstructed glycosidase

Keywords

HYDROLASE / Ancestral reconstructed / glycosidase /

Family 1 /

heme

Function / homology

PROTOPORPHYRIN IX CONTAINING FE

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.45 Å

Authors

Gavira, J.A. / Risso, V.A. / Sanchez-Ruiz, J.M. / Gamiz-Arco, G. / Gutierrez-Rus, L. / Ibarra-Molero, B. / Oshino, Y. / Petrovic, D. / Romero-Rivera, A. / Seelig, B. ...

Funding support

United States,

Spain, 2items

Citation

Journal: Nat Commun / Year: 2021
Title: Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase.
Authors: Gamiz-Arco, G. / Gutierrez-Rus, L.I. / Risso, V.A. / Ibarra-Molero, B. / Hoshino, Y. / Petrovic, D. / Justicia, J. / Cuerva, J.M. / Romero-Rivera, A. / Seelig, B. / Gavira, J.A. / Kamerlin, ...

History

Deposition	May 14, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 27, 2021	Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn Item: _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id ..._struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6z1m.cif.gz	653.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6z1m.ent.gz	454.5 KB	Display	PDB format
PDBx/mmJSON format	6z1m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z1/6z1m ftp://data.pdbj.org/pub/pdb/validation_reports/z1/6z1m	HTTPS FTP

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Related structure data

Related structure data	6z1hC 2j78S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6w8h-d 4ohj-1 2cvd-2 4ee0-d 3lg6-2 2imk-d 4ohj-2 1a0f-d 2pmt-1 2vcw-1 Search similar-shape structures by Omokage search (details) 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ancestral reconstructed glycosidase

B: Ancestral reconstructed glycosidase

C: Ancestral reconstructed glycosidase

hetero molecules

161 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ancestral reconstructed glycosidase

hetero molecules

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

2

B: Ancestral reconstructed glycosidase

hetero molecules

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

3

C: Ancestral reconstructed glycosidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.934, 89.496, 141.120
Angle α, β, γ (deg.)	90.000, 94.211, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 3 molecules ABC

#1: Protein	Ancestral reconstructed glycosidase Mass: 52610.605 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 173 molecules

#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.97 Å³/Da / Density % sol: 37.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: HRI (#9): 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v PEG 4.000

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.45→55.32 Å / Num. obs: 53447 / % possible obs: 99.02 % / Redundancy: 3.2 % / B_iso Wilson estimate: 50.34 Å² / CC_1/2: 0.997 / Net I/σ(I): 10.15
Reflection shell	Resolution: 2.45→2.54 Å / Mean I/σ(I) obs: 1.44 / Num. unique obs: 5335 / CC_1/2: 0.718

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Processing

Software

Name	Version	Classification
Coot		model building
PHENIX	1.15.2_3472	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2J78

2j78

Resolution: 2.45→55.32 Å / SU ML: 0.3109 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2206	2666	4.99 %
R_work	0.1754	50742	-
obs	0.1776	53408	99.03 %

Solvent computation

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

Displacement parameters

B_iso mean: 62.81 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→55.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10248	0	212	156	10616

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0049	11193
X-RAY DIFFRACTION	f_angle_d	0.7191	15217
X-RAY DIFFRACTION	f_chiral_restr	0.0449	1497
X-RAY DIFFRACTION	f_plane_restr	0.0039	2001
X-RAY DIFFRACTION	f_dihedral_angle_d	6.8727	8834

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 (%)
2.45-2.49	0.276	148	0.2519	2636	X-RAY DIFFRACTION	99.5
2.49-2.54	0.331	132	0.2556	2696	X-RAY DIFFRACTION	99.68
2.54-2.59	0.3219	152	0.2583	2648	X-RAY DIFFRACTION	99.61
2.59-2.65	0.3016	129	0.2516	2695	X-RAY DIFFRACTION	99.44
2.65-2.71	0.2998	144	0.2503	2647	X-RAY DIFFRACTION	99.43
2.71-2.78	0.3189	150	0.2435	2630	X-RAY DIFFRACTION	99.04
2.78-2.86	0.3322	131	0.2413	2686	X-RAY DIFFRACTION	99.26
2.86-2.94	0.2524	148	0.2241	2666	X-RAY DIFFRACTION	98.98
2.94-3.03	0.2736	134	0.2127	2652	X-RAY DIFFRACTION	99.71
3.03-3.14	0.2776	162	0.1981	2695	X-RAY DIFFRACTION	99.44
3.14-3.27	0.2679	126	0.1985	2689	X-RAY DIFFRACTION	99.47
3.27-3.42	0.2382	118	0.193	2671	X-RAY DIFFRACTION	99.22
3.42-3.6	0.2166	141	0.1694	2656	X-RAY DIFFRACTION	98.73
3.6-3.82	0.2124	149	0.1557	2676	X-RAY DIFFRACTION	98.91
3.82-4.12	0.1918	155	0.1431	2654	X-RAY DIFFRACTION	98.42
4.12-4.53	0.1672	124	0.1347	2652	X-RAY DIFFRACTION	97.61
4.53-5.19	0.1794	138	0.1343	2660	X-RAY DIFFRACTION	98.52
5.19-6.53	0.2066	138	0.1634	2707	X-RAY DIFFRACTION	98.72
6.53-55.32	0.1689	147	0.1583	2726	X-RAY DIFFRACTION	98.05

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	2.38695259759	0.156330484136	0.0629603336361	2.19678591472	0.671707073266	2.87589242468	-0.0297076171003	-0.0442986417099	-0.236351144821	0.199822803682	-0.00587387983795	0.0389881896968	0.511981390442	0.22904084715	0.0396564822111	0.406946366886	0.0340831860696	0.0141093568355	0.341089882744	0.0186991749165	0.379864777847	2.47886493157	-4.40510080111	17.0340882619
2	6.02357369449	2.56154834457	-1.62301301002	4.62773209844	-1.51214463156	3.95569840072	-0.142839542156	0.231266446253	-0.159779805469	-0.454134906156	-0.0593106372928	-0.473996788524	-0.0805670605368	0.77354939204	0.206023653107	0.460995724735	0.0448903570846	0.0345274875817	0.618871838298	0.0163132328119	0.351698219026	13.3584815701	-0.0352777226869	0.0663193718899
3	1.73592988024	0.190792281221	0.0142083536491	2.5803792499	0.463922130877	3.25388211588	0.0580618972389	0.297787490563	0.0180946467356	-0.390941416857	-0.119029296133	0.210437078843	-0.243913021311	-0.190723820655	0.0967409431388	0.287435455529	-0.00148103270283	-0.0390595464494	0.403131703622	-0.000360461713039	0.391824944402	-6.25149650328	5.31849053453	5.37294823197
4	8.08118462858	-2.86220318956	6.23513659552	4.58663821013	0.972552488559	1.99987584419	-0.00579226592842	-0.0584585466772	0.0250769330194	-0.0797049539707	-0.0236954492378	0.00807917713122	-0.026644593094	0.187959381686	0.0276552307328	1.00875527771	0.100206422764	-0.0227641950945	1.56418907235	0.0854598165226	1.46685519337	-24.4811373828	8.20110318081	-0.403129100593
5	1.57853172701	0.165543174323	0.0532113135195	1.60557779528	-0.22586381017	2.36892075729	-0.0329119590499	-0.0314937164788	-0.182589945691	0.0979541681293	0.139049695005	-0.202688489512	0.0786582604614	-0.0294741950359	-0.0906457792659	0.273487951628	0.0471727928535	-0.0331317381778	0.361667962587	-0.0387849258637	0.355458629953	-20.847327864	10.6284281557	47.6266993124
6	1.79402830028	-0.0462921856924	1.55041571394	3.1739420404	-2.32416185971	3.31706069814	-0.0593568461277	0.109818784997	-0.0222520528198	0.283428641936	0.234204198127	0.0969631743082	-0.128481082831	-0.5199259527	-0.16072612029	0.45090934394	-0.0335908277465	-0.0396101880468	0.621129332342	-0.009705148122	0.453120499144	-39.1594721599	9.56511409174	42.2129622005
7	2.50684910489	0.632543532103	0.372804440967	2.8747801403	-0.0216865634322	3.23501708467	0.107105847636	-0.408623889843	-0.281272025935	0.579739586191	0.00777507585405	-0.0107521306502	0.292139985883	-0.448472474677	-0.0961890277778	0.365142511422	0.0189191404712	-0.0129238067387	0.442267171871	0.0660572688501	0.328780387529	-30.8630750535	4.57649239555	64.1852200816
8	1.36256448328	0.489411095011	-0.275811322114	1.78288505125	-0.23228105324	1.46309102004	0.0389101656437	-0.102191864996	0.276185804781	0.304610172208	0.0324307463064	0.232421986538	-0.438740646835	-0.178845373353	-0.0496313301383	0.522666306676	0.091767742211	0.0151138456389	0.398373978435	0.00249640814624	0.418008531763	-14.8199271481	45.9580371214	44.1743122302
9	4.08259405552	-1.52647314672	-1.01113560424	7.3120345992	1.79739322274	6.1252890019	-0.0439245654985	0.291744888216	0.112160416522	-0.219714083215	0.102245362757	-0.278672324396	-0.0756318719364	0.0745140163945	-0.0223712449465	0.442817590197	-0.0751873690018	-0.0135144983392	0.400094230525	0.00812247874122	0.385782308664	-9.74038109054	43.2176211105	24.5611044971
10	2.46006462984	0.187279167832	0.841121422903	1.98414865448	-0.3127150996	3.18376635326	0.0491620432648	0.111899946317	0.274023625074	-0.139086152943	-0.0671461585995	0.0341356875009	-0.353772729841	0.202170069534	0.0377120836928	0.545759744614	0.00910985499285	-0.00257927022845	0.30494176086	-0.0327777034885	0.35088606142	-0.0258010331664	51.6773299616	39.6880972772
11	8.90717338983	-8.00849236499	-5.58719812685	7.24781663039	4.98343785349	3.53772694996	0.184926885461	-0.0373191496399	0.0873264185593	0.0472370996598	-0.383983460266	0.285480327131	0.265623894979	-0.630160507169	0.269034331182	1.66773877276	-0.111463734398	0.0626347570854	1.16875372949	0.215602506218	1.47208241759	14.4470064469	66.8020505149	44.3460879945

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 216 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 217 through 278 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 279 through 450 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 451 through 451 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 8 through 216 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 217 through 350 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 351 through 450 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 7 through 216 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 217 through 271 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 272 through 450 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 451 through 451 )

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