PDB-6x9y: The crystal structure of a Beta-lactamase from Escherichia coli CFT073

ID or keywords:

Entry

Database: PDB / ID: 6x9y

Title

The crystal structure of a Beta-lactamase from Escherichia coli CFT073

Components

Beta-lactamase

Keywords

HYDROLASE / Beta-lactamase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function

Biological species

Escherichia coli O6:H1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Tan, K. / Wu, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The crystal structure of a Beta-lactamase from Escherichia coli CFT073
Authors: Tan, K. / Wu, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jun 3, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6x9y.cif.gz	356.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6x9y.ent.gz	241.8 KB	Display	PDB format
PDBx/mmJSON format	6x9y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6x9y_validation.pdf.gz	467.5 KB	Display	wwPDB validaton report
Full document	6x9y_full_validation.pdf.gz	472.5 KB	Display
Data in XML	6x9y_validation.xml.gz	28.9 KB	Display
Data in CIF	6x9y_validation.cif.gz	41.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x9/6x9y ftp://data.pdbj.org/pub/pdb/validation_reports/x9/6x9y	HTTPS FTP

-
Related structure data

Similar structure data	1my8-2 4e3m-2 3gr2-1 3gvb-1 6n9k-2 4kg6-3 5ggw-1 1bls-1 4kz6-1 1kvm-2 2pu2-2 5ggw-2 3fkv-1 1fco-2 3bls-2 6dpy-2 1ke4-2 4okp-2 4kz3-1 4kz3-2 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
Other databases	TargetTrack: IDP97191

Similar structure data

Other databases

TargetTrack: IDP97191

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#29 - May 2002 Penicillin-binding Proteins similarity (3) #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) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	128.176, 128.176, 92.761
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃
Space group name Hall	P6c
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/2 #3: y,-x+y,z+1/2 #4: -y,x-y,z #5: -x+y,-x,z #6: -x,-y,z+1/2

#1: Protein	Beta-lactamase Mass: 39859.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria) Strain: CFT073 / ATCC 700928 / UPEC / Gene: ampC, c5238 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0H2VDE7, UniProt: P00811*PLUS, beta-lactamase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-SRT / S,R MESO-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₆
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.54 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Sodium Acetate, 0.1 M HEPES: NaOH, 25 % (w/v) PEG 4000, 0.2 M Lithium Sulfate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97927 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2018
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97927 Å / Relative weight: 1
Reflection	Resolution: 1.9→47.6 Å / Num. obs: 68159 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / B_iso Wilson estimate: 31.5729232094 Å² / CC_1/2: 0.991 / CC star: 0.998 / R_merge(I) obs: 0.084 / R_pim(I) all: 0.035 / R_rim(I) all: 0.091 / Χ²: 1.086 / Net I/σ(I): 27.58
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.715 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 3396 / CC_1/2: 0.851 / CC star: 0.959 / R_pim(I) all: 0.296 / R_rim(I) all: 0.77 / Χ²: 0.484 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
PHENIX	1.10.1_2155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.9→47.6 Å / SU ML: 0.178693821941 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.1759964247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.198	3325	4.88 %	random
R_work	0.161	64790	-	-
obs	0.162	68115	99.28 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 41.49 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→47.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5579	0	77	240	5896

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0121277172556	5813
X-RAY DIFFRACTION	f_angle_d	1.15432786212	7939
X-RAY DIFFRACTION	f_chiral_restr	0.0744872545217	860
X-RAY DIFFRACTION	f_plane_restr	0.00771668142504	1014
X-RAY DIFFRACTION	f_dihedral_angle_d	13.8517800304	3404

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 (%)
1.9-1.9235	0.270951297248	137	0.21651246496	2265	X-RAY DIFFRACTION	83.986013986
1.9235-1.9522	0.280797376746	134	0.199492836696	2702	X-RAY DIFFRACTION	100
1.9522-1.9827	0.232044099822	141	0.183998358349	2689	X-RAY DIFFRACTION	99.8588567396
1.9827-2.0152	0.213546544803	144	0.185734100562	2699	X-RAY DIFFRACTION	99.9297012302
2.0152-2.0499	0.212337121419	136	0.172083073619	2721	X-RAY DIFFRACTION	100
2.0499-2.0872	0.254910304356	173	0.16823896028	2671	X-RAY DIFFRACTION	99.9648506151
2.0872-2.1274	0.20327125742	118	0.165545455557	2723	X-RAY DIFFRACTION	99.9648135116
2.1274-2.1708	0.203453122477	134	0.160331214465	2741	X-RAY DIFFRACTION	100
2.1708-2.218	0.208209094594	126	0.155736493512	2686	X-RAY DIFFRACTION	99.9644507643
2.218-2.2696	0.193175811317	156	0.157059380975	2699	X-RAY DIFFRACTION	100
2.2696-2.3263	0.221186853472	145	0.159291962821	2732	X-RAY DIFFRACTION	99.9652536484
2.3263-2.3892	0.191267308474	143	0.16514435118	2697	X-RAY DIFFRACTION	99.9296270232
2.3892-2.4595	0.17728999315	127	0.167453498316	2710	X-RAY DIFFRACTION	99.9647639183
2.4595-2.5389	0.204229116852	131	0.166525977059	2710	X-RAY DIFFRACTION	99.9648135116
2.5389-2.6296	0.230366106249	111	0.17419740099	2753	X-RAY DIFFRACTION	100
2.6296-2.7349	0.225474386362	152	0.177364389747	2722	X-RAY DIFFRACTION	100
2.7349-2.8594	0.218802870012	140	0.182535577238	2692	X-RAY DIFFRACTION	99.9294283698
2.8594-3.0101	0.24954340541	120	0.183511225722	2738	X-RAY DIFFRACTION	100
3.0101-3.1987	0.213346336096	132	0.177131221191	2737	X-RAY DIFFRACTION	99.8955431755
3.1987-3.4456	0.202904273944	152	0.182644745304	2720	X-RAY DIFFRACTION	100
3.4456-3.7922	0.183877685249	127	0.154533994872	2729	X-RAY DIFFRACTION	100
3.7922-4.3406	0.174209179528	148	0.140822467539	2733	X-RAY DIFFRACTION	99.9306278182
4.3406-5.4674	0.185099413221	150	0.131749743529	2748	X-RAY DIFFRACTION	99.9655053467
5.4674-47.6	0.158535288406	148	0.145577934361	2773	X-RAY DIFFRACTION	99.5229982964

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	3.76834818891	1.21658300459	0.851149631178	3.27974763844	5.07789351725	8.21396378185	-0.272658919052	-0.689814166361	0.376171100366	1.05422655033	0.674151679406	-1.53995063032	-0.130326905808	0.820715866651	-0.372774617213	0.366062821172	0.00102654967143	-0.187778287348	0.575663957256	-0.0416768106126	0.69685384645	16.3753966503	-46.836998216	16.8821594071
2	2.84581649265	-1.37578254166	0.00741410700263	2.32845401893	0.0676227907419	0.609896990364	0.241136234443	0.154359003499	0.275490419287	-0.291014886294	-0.207973210429	-0.50855577055	-0.0419159529041	0.0446578043554	-0.0112640336572	0.277034141577	0.00154857034605	0.0915374642535	0.260999762515	0.0612742340536	0.307578796805	4.60377763494	-44.1947511239	-2.87828516589
3	3.13343028921	-0.26680115518	-0.439582987793	3.69009620617	0.380924780018	3.15860916315	0.187666692861	0.556528146909	-0.602521765242	-0.489523319772	-0.178874824044	0.333504094358	0.206112879713	-0.127500493311	0.0200149779443	0.257216938543	0.0543632401005	-0.0600294596957	0.312063157097	-0.0772530584311	0.296507921056	-13.2125847418	-54.4934495381	-9.13440381144
4	2.83891450629	-1.02308876883	0.0633124372714	2.38606570257	0.405003700028	0.624866764525	0.1191893777	0.0699048120526	0.22266161321	-0.123549418822	-0.0959463358703	-0.47326253988	-0.120631508767	0.0363720498078	-0.0220823998476	0.232748012747	-0.0140420413203	0.0375953657347	0.226767875576	0.0421832903994	0.25594949913	1.3133873586	-43.8265790163	1.6538788576
5	3.73861869702	3.71803190124	-4.22869443301	6.81733128794	-1.93110419839	8.7046115776	0.705619234176	1.29898613397	1.52259317365	-0.814057998498	-0.0932337822509	0.265254831554	-0.920454296751	0.00404661503494	-0.464422782255	0.590117120167	0.158815358891	0.0607485415737	0.437129231953	0.158981826469	0.670522052721	-46.8946653028	-10.0758623944	-16.634838058
6	3.03764607853	-0.909946185969	0.153817582751	1.59996914548	0.0115224022273	1.01071997128	0.0142425841739	-0.156682310218	0.959068505331	-0.0400232753329	0.0633338490377	-0.107836337803	-0.250929161139	-0.00549267078073	-0.083947557707	0.310740215996	-0.010012562775	0.0271872918741	0.235343351181	-0.0660336220229	0.547282426671	-43.3875041038	-12.7293890911	-1.23705993864
7	3.28525367819	-0.305058949217	-0.0109745857419	3.01214325207	0.54820363734	1.82343181062	-0.189483837096	-0.828073923394	-0.160047030852	0.458679255283	0.217791457694	0.23264450229	0.0113669689986	0.138257056104	0.00612846668685	0.280690255404	0.0710629128328	0.0237391291158	0.421271070397	0.0116111365516	0.191506731392	-37.0455849846	-36.9933543107	11.7344788403
8	3.57010504486	-0.938083008022	0.102574583802	1.89011868911	-0.292613271814	0.928970948047	-0.0637391370671	-0.776033519984	0.938395263069	0.217468117314	0.243154909415	0.00639163589355	-0.177687678736	0.0202232291893	-0.156343962714	0.40167555016	0.0131369245799	0.0243628846572	0.395577293982	-0.22113812416	0.609729212266	-46.3978926737	-13.1186465137	8.51945440446
9	3.15062642108	-1.17582389556	-0.379122705045	2.18936736586	-0.0873288864267	0.766974756217	0.102964813593	0.024173837234	0.502258688113	-0.15800333047	-0.0218505469634	-0.144776723433	-0.103563599177	0.117214990606	-0.0837759288569	0.236726432984	-0.00826983065517	-0.00322144623175	0.234537571094	-0.0188265263614	0.236310963528	-36.4347183516	-24.1810456903	-5.34270669293

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 31 through 50 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 51 through 125 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 126 through 189 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 190 through 388 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 30 through 50 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 51 through 106 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 107 through 204 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 205 through 236 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 237 through 388 )

-
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