PDB-5twe: CTX-M-14 P167S:S70G mutant enzyme crystallized with ceftazidime

ID or keywords:

Entry

Database: PDB / ID: 5twe

Title

CTX-M-14 P167S:S70G mutant enzyme crystallized with ceftazidime

Components

Beta-lactamase

Keywords

HYDROLASE/ANTIBIOTIC / CTX-M beta-lactamase ceftazidime / HYDROLASE-ANTIBIOTIC complex

Function / homology

Function and homology information

beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.5 Å

Authors

Patel, M. / Stojanoski, V. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2017
Title: The Drug-Resistant Variant P167S Expands the Substrate Profile of CTX-M beta-Lactamases for Oxyimino-Cephalosporin Antibiotics by Enlarging the Active Site upon Acylation.
Authors: Patel, M.P. / Hu, L. / Stojanoski, V. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.

History

Deposition	Nov 12, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 28, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 19, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 4, 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

-
Download

PDBx/mmCIF format	5twe.cif.gz	123 KB	Display	PDBx/mmCIF format
PDB format	pdb5twe.ent.gz	93.1 KB	Display	PDB format
PDBx/mmJSON format	5twe.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5twe_validation.pdf.gz	756.2 KB	Display	wwPDB validaton report
Full document	5twe_full_validation.pdf.gz	757.4 KB	Display
Data in XML	5twe_validation.xml.gz	15.3 KB	Display
Data in CIF	5twe_validation.cif.gz	23.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tw/5twe ftp://data.pdbj.org/pub/pdb/validation_reports/tw/5twe	HTTPS FTP

-
Related structure data

Related structure data	5tw6C 5twdC 5u53C 5vthC 1yltS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6v83-d 6cyn-2 6cyq-3 6v6g-d 6cyu-d 4dds-2 1ymx-2 5t66-1 4pm9-d 5tw6-d 6h2h-1 5ll7-d 1yly-2 7k2y-d 6qwe-d 4de2-1 6jn3-1 5vth-d 7k2x-5 6v8v-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	#164 - Aug 2013 Serotonin Receptor similarity (5) #29 - May 2002 Penicillin-binding Proteins similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2)

Deposited unit

A: Beta-lactamase

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	41.610, 41.610, 232.234
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-686- HOH

#1: Protein	Beta-lactamase Mass: 27960.482 Da / Num. of mol.: 1 / Fragment: UNP residues 29-291 / Mutation: S70G, P167S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AN206_26770, APT94_14605, BJJ90_27545, BK334_27290, ...Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, AN206_26770, APT94_14605, BJJ90_27545, BK334_27290, ETN48_p0088, pCT_085, pHK01_011 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9L5C7, beta-lactamase
#2: Chemical	ChemComp-CAZ / ACYLATED CEFTAZIDIME Mass: 469.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₁₉N₅O₇S₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M lithium acetate, 20% (w/v) PEG 3350

-
Data collection

Diffraction

Mean temperature: 293 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.97 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.97 Å / Relative weight: 1

Reflection

Resolution: 1.5→34.43 Å / Num. obs: 71895 / % possible obs: 99.2 % / Redundancy: 6.4 % / CC_1/2: 0.917 / R_merge(I) obs: 0.214 / R_pim(I) all: 0.099 / R_rim(I) all: 0.238 / Net I/σ(I): 6 / Num. measured all: 123391 / Scaling rejects: 537

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.9-1.94	8	0.301	9410	1170	0.897	0.112	0.322	5	99.8
9.11-38.7	5.7	0.097	1084	191	0.979	0.045	0.108	8.5	83.2

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
Aimless	0.5.1	data scaling
PDB_EXTRACT	3.2	data extraction
MOLREP		phasing
MOSFLM		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1YLT

1ylt

Resolution: 1.5→30.617 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.75 / Phase error: 14.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1692	3619	5.03 %	RANDOM
R_work	0.1502	-	-	-
obs	0.1511	71895	99.8 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5→30.617 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1952	0	31	324	2307

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2035
X-RAY DIFFRACTION	f_angle_d	1.46	2778
X-RAY DIFFRACTION	f_dihedral_angle_d	8.586	1675
X-RAY DIFFRACTION	f_chiral_restr	0.063	328
X-RAY DIFFRACTION	f_plane_restr	0.005	367

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 (%)
1.5-1.5198	0.1909	157	0.1847	2583	X-RAY DIFFRACTION	100
1.5198-1.5406	0.2005	146	0.1662	2711	X-RAY DIFFRACTION	100
1.5406-1.5626	0.1835	109	0.1666	2610	X-RAY DIFFRACTION	100
1.5626-1.5859	0.1632	143	0.1612	2613	X-RAY DIFFRACTION	100
1.5859-1.6107	0.1921	139	0.163	2626	X-RAY DIFFRACTION	100
1.6107-1.6371	0.1558	116	0.1566	2657	X-RAY DIFFRACTION	100
1.6371-1.6653	0.1737	140	0.1581	2722	X-RAY DIFFRACTION	100
1.6653-1.6956	0.1813	144	0.1556	2499	X-RAY DIFFRACTION	100
1.6956-1.7282	0.205	137	0.1566	2699	X-RAY DIFFRACTION	100
1.7282-1.7635	0.1878	149	0.1552	2586	X-RAY DIFFRACTION	100
1.7635-1.8018	0.1812	162	0.1576	2644	X-RAY DIFFRACTION	100
1.8018-1.8438	0.1822	109	0.1536	2626	X-RAY DIFFRACTION	100
1.8438-1.8899	0.143	141	0.1573	2710	X-RAY DIFFRACTION	100
1.8899-1.9409	0.2007	104	0.1523	2570	X-RAY DIFFRACTION	100
1.9409-1.9981	0.1695	109	0.1554	2702	X-RAY DIFFRACTION	100
1.9981-2.0625	0.1911	145	0.1435	2611	X-RAY DIFFRACTION	100
2.0625-2.1362	0.1487	141	0.1419	2601	X-RAY DIFFRACTION	100
2.1362-2.2217	0.1623	172	0.1407	2606	X-RAY DIFFRACTION	100
2.2217-2.3228	0.1517	158	0.1442	2676	X-RAY DIFFRACTION	100
2.3228-2.4452	0.1736	160	0.1533	2610	X-RAY DIFFRACTION	100
2.4452-2.5984	0.1609	160	0.1487	2591	X-RAY DIFFRACTION	100
2.5984-2.7989	0.1936	134	0.1549	2595	X-RAY DIFFRACTION	100
2.7989-3.0803	0.1592	151	0.148	2591	X-RAY DIFFRACTION	100
3.0803-3.5254	0.1442	135	0.1413	2662	X-RAY DIFFRACTION	100
3.5254-4.4395	0.1475	144	0.1342	2613	X-RAY DIFFRACTION	100
4.4395-30.6236	0.2009	114	0.1622	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	5.5267	0.5685	0.8891	2.2344	-0.0042	2.4562	-0.0189	0.2158	0.315	-0.2994	-0.0766	-0.0856	-0.5185	0.0992	0.0797	0.2138	0.005	0.0348	0.1433	0.0188	0.0923	-3.6265	16.7463	-31.4991
2	1.4583	-1.3153	0.7173	0.9626	-0.5562	1.3662	-0.0457	0.0724	0.2417	0.0567	-0.0885	-0.1781	-0.2988	0.3044	0.1014	0.1078	-0.047	0.003	0.1586	0.0118	0.1315	5.13	10.5836	-16.4732
3	5.9006	2.7254	1.5846	5.8803	1.0608	2.9453	0.2306	-0.4358	-0.4699	0.4232	-0.148	-0.4646	0.3026	0.3966	-0.0781	0.1713	0.0587	-0.0053	0.238	-0.0083	0.1032	12.2936	-10.3024	-5.0331
4	1.3286	-0.7184	-0.2811	2.436	0.0127	1.975	0.0557	0.0465	-0.1721	-0.1136	-0.0655	0.0175	0.2201	0.2079	0.0036	0.0688	0.0299	-0.0028	0.1313	-0.012	0.0978	6.0069	-6.2703	-11.4734
5	2.5933	-0.5093	0.3727	1.2466	-1.2863	2.0988	0.0364	0.0348	-0.1318	-0.0624	0.0824	0.0802	-0.033	-0.0765	-0.1087	0.1016	0.0121	0.0191	0.1372	-0.0022	0.1374	-5.7312	4.8745	-11.3561
6	5.807	-1.749	-0.4359	0.7984	-0.0211	1.6674	-0.2056	0.1451	0.3144	0.1124	0.0434	-0.2318	-0.3055	0.3313	0.1122	0.1192	-0.0584	-0.0155	0.149	0.0228	0.1179	6.0385	13.6071	-16.8283
7	1.2294	-0.651	0.6667	0.8203	-0.283	1.1759	0.1753	0.4657	0.044	-0.1379	-0.1666	-0.1526	0.0734	0.5336	0.0431	0.0602	0.0139	0.0496	0.3462	0.0253	0.1	10.0831	4.3804	-23.7511
8	5.906	1.2077	-0.3919	2.5181	-0.2787	2.1381	0.0454	0.2817	-0.0497	-0.2987	-0.1481	-0.1045	-0.0384	0.2942	0.0802	0.0885	0.0145	0.0448	0.1994	0.053	0.0545	-0.5655	7.6838	-27.5707
9	6.7235	2.2116	-1.3474	2.2129	-0.5216	2.277	-0.0013	0.5904	0.1607	-0.3097	-0.0418	-0.0623	-0.4131	0.3723	0.0769	0.1955	-0.0304	0.0169	0.3038	0.0323	0.0816	2.3231	10.5835	-34.9591

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 26 through 50 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 51 through 86 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 87 through 101 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 102 through 155 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 156 through 179 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 180 through 194 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 195 through 251 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 252 through 275 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 276 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://pdbjlvh1.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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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