PDB-3zdj: Ancestral (ENCA) beta-lactamase class A

ID or keywords:

Entry

Database: PDB / ID: 3zdj

Title

Ancestral (ENCA) beta-lactamase class A

Components

ENCA BETA-LACTAMASE

Keywords

HYDROLASE / ANTIBIOTIC RESISTANCE

Function / homology

Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta

Function and homology information

Biological species

SYNTHETIC CONSTRUCT (others)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Gavira, J.A. / Risso, V.A. / Sanchez-Ruiz, J.M.

Citation

Journal: J.Am.Chem.Soc. / Year: 2013
Title: Hyperstability and Substrate Promiscuity in Laboratory Resurrections of Precambrian Beta-Lactamases.
Authors: Risso, V.A. / Gavira, J.A. / Mejia-Carmona, D.F. / Gaucher, E.A. / Sanchez-Ruiz, J.M.

History

Deposition	Nov 27, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 20, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 27, 2013	Group: Atomic model / Other
Revision 1.2	Mar 27, 2013	Group: Database references
Revision 1.3	Mar 6, 2019	Group: Data collection / Experimental preparation / Other Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3zdj.cif.gz	312.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3zdj.ent.gz	263 KB	Display	PDB format
PDBx/mmJSON format	3zdj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3zdj_validation.pdf.gz	443 KB	Display	wwPDB validaton report
Full document	3zdj_full_validation.pdf.gz	445.1 KB	Display
Data in XML	3zdj_validation.xml.gz	21.6 KB	Display
Data in CIF	3zdj_validation.cif.gz	30.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zd/3zdj ftp://data.pdbj.org/pub/pdb/validation_reports/zd/3zdj	HTTPS FTP

-
Related structure data

Related structure data	4b88C 2qpnS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4mbk-d 2h0t-d 3hiv-2 1jvj-d 4xuz-d 1q2p-d 3opr-d 3oph-d 1shv-d 6lor-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 - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ENCA BETA-LACTAMASE

B: ENCA BETA-LACTAMASE

hetero molecules

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

1

A: ENCA BETA-LACTAMASE

hetero molecules

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

2

B: ENCA BETA-LACTAMASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	111.144, 111.144, 93.722
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	172
Space group name H-M	P6₄

#1: Protein	ENCA BETA-LACTAMASE Mass: 28598.643 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: RESURRECTED SEQUENCE, ANCESTRAL RECONSTRUCTED / Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: beta-lactamase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	RESIDUE NUMBERING IS BASED ON R.P.AMBLER ET AL. (BIOCHEM. J., V. 276, P. 269, 1991).

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 57 % / Description: NONE
Crystal grow	Method: counter-diffusion Details: COUNTER-DIFFUSION, 2M LI-SULPHATE, 0.1M NA-HEPES PH 7.50

-
Data collection

Diffraction	Mean temperature: 297 K
Diffraction source	Source: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54
Detector	Type: BRUKER SMART 6000 / Detector: CCD / Date: Oct 10, 2012 / Details: MONTEL OPTICS
Radiation	Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.4→48.13 Å / Num. obs: 26073 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 21.17 % / B_iso Wilson estimate: 34.2 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 15.38
Reflection shell	Resolution: 2.4→2.49 Å / Redundancy: 20.93 % / R_merge(I) obs: 0.57 / Mean I/σ(I) obs: 1.73 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
SAINT		data reduction
SADABS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QPN

2qpn

Resolution: 2.4→48.127 Å / SU ML: 0.23 / σ(F): 1.97 / Phase error: 19.41 / Stereochemistry target values: ML / Details: MET AT POSITION 25 IS A PURIFICATION ARTEFACT

	R_factor	Num. reflection	% reflection
R_free	0.1786	2569	5.1 %
R_work	0.1599	-	-
obs	0.1626	25770	99.68 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→48.127 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3992	0	20	171	4183

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	4285
X-RAY DIFFRACTION	f_angle_d	1.296	5851
X-RAY DIFFRACTION	f_dihedral_angle_d	15.834	1631
X-RAY DIFFRACTION	f_chiral_restr	0.072	682
X-RAY DIFFRACTION	f_plane_restr	0.006	768

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 (%)
2.4001-2.4463	0.2814	157	0.2751	2674	X-RAY DIFFRACTION	100
2.4463-2.4962	0.2796	133	0.2565	2681	X-RAY DIFFRACTION	100
2.4962-2.5505	0.3003	146	0.2493	2687	X-RAY DIFFRACTION	100
2.5505-2.6098	0.2641	141	0.2331	2645	X-RAY DIFFRACTION	100
2.6098-2.6751	0.261	152	0.2299	2679	X-RAY DIFFRACTION	100
2.6751-2.7474	0.2536	139	0.2245	2681	X-RAY DIFFRACTION	100
2.7474-2.8282	0.2381	153	0.2233	2645	X-RAY DIFFRACTION	100
2.8282-2.9195	0.2473	124	0.2089	2703	X-RAY DIFFRACTION	100
2.9195-3.0238	0.2104	175	0.2061	2635	X-RAY DIFFRACTION	100
3.0238-3.1449	0.2003	127	0.1911	2672	X-RAY DIFFRACTION	100
3.1449-3.288	0.1966	129	0.1795	2693	X-RAY DIFFRACTION	100
3.288-3.4613	0.1947	147	0.1518	2672	X-RAY DIFFRACTION	100
3.4613-3.6781	0.168	125	0.1332	2657	X-RAY DIFFRACTION	100
3.6781-3.9619	0.125	143	0.1309	2690	X-RAY DIFFRACTION	100
3.9619-4.3604	0.1273	140	0.1082	2645	X-RAY DIFFRACTION	100
4.3604-4.9908	0.1194	152	0.1043	2658	X-RAY DIFFRACTION	100
4.9908-6.2856	0.1545	139	0.1421	2675	X-RAY DIFFRACTION	100
6.2856-48.1364	0.1527	147	0.1395	2562	X-RAY DIFFRACTION	96

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	1.6583	0.3776	-0.835	2.6749	1.7885	1.9369	0.1503	-0.2427	0.2757	0.4807	-0.1264	0.3217	0.1614	-0.0325	0.0518	0.3155	-0.0403	0.1875	0.343	0.0131	0.3117	68.267	65.672	-66.1179
2	0.9094	0.0728	0.0789	1.2839	-0.0411	0.4102	-0.0429	0.122	0.1902	0.1056	0.1647	0.3099	-0.0668	-0.182	-0.075	0.2111	0.0604	0.1314	0.3009	0.0865	0.3065	71.9077	68.9378	-80.2135
3	0.7417	-0.0898	0.027	0.9657	0.1396	0.9248	0.3563	-0.1014	0.3803	-0.1288	-0.0249	-0.0729	-0.6687	0.4598	-0.1355	0.2451	-0.1092	0.063	0.2799	0.1311	0.2071	95.734	78.6232	-90.1014
4	3.5552	-0.3853	-1.1033	3.0206	0.372	1.8116	0.2673	-0.7335	0.6616	0.7026	0.0142	-0.4838	-0.6583	0.4791	-0.1779	0.5661	-0.1718	-0.0159	0.3217	-0.0401	0.3232	99.8087	88.7861	-79.4861
5	1.0944	0.6071	-0.422	1.302	-0.0822	1.4141	0.0922	0.0635	0.2525	0.117	-0.0258	0.2135	-0.3516	-0.1303	-0.0565	0.2074	0.0387	0.0498	0.1727	0.0792	0.2283	83.9199	79.2849	-87.4436
6	2.075	0.009	-0.8885	0.8203	-0.0516	2.0988	-0.0457	-0.1791	-0.0061	0.2863	-0.0396	0.031	0.0704	0.1288	0.0662	0.1795	0.0196	0.0324	0.1624	0.0548	0.1357	87.2213	68.2276	-77.6625
7	1.9303	-0.0936	0.0138	2.1695	0.8642	2.8804	-0.0127	-0.125	0.466	0.4924	0.009	0.3082	-0.3911	-0.2984	0.072	0.2824	0.1141	0.1279	0.1907	-0.001	0.3088	74.4472	75.4921	-74.0166
8	1.8115	1.0302	0.0832	8.5007	-0.0665	1.0679	0.2167	-0.2464	0.1405	0.964	-0.3268	0.0833	0.0481	-0.1276	0.0957	0.3213	0.0021	0.0985	0.2846	0.0469	0.1914	76.8333	68.9371	-67.3051
9	1.2607	-0.0562	0.1235	1.5134	0.0661	1.1015	-0.1357	0.2856	0.01	-0.3789	0.162	0.0788	-0.1036	0.033	-0.0346	0.212	-0.1208	-0.0203	0.2638	0.0799	0.1861	95.051	72.9062	-119.6584
10	2.1005	0.8506	-0.4977	2.3862	-0.4881	1.0276	-0.2665	0.4047	-0.1952	-0.445	0.3084	0.0747	0.1204	0.0031	-0.0287	0.207	-0.119	-0.0096	0.2519	0.0151	0.1449	96.3366	67.1456	-120.0949

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 25 THROUGH 39 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 40 THROUGH 68 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 69 THROUGH 98 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 99 THROUGH 118 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 119 THROUGH 195 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 196 THROUGH 258 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 259 THROUGH 271 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 272 THROUGH 290 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 25 THROUGH 98 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 99 THROUGH 290 )

-
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