PDB-6whf: class C beta-lactamase from Escherichia coli in complex with ceph...

ID or keywords:

Entry

Database: PDB / ID: 6whf

Title

class C beta-lactamase from Escherichia coli in complex with cephalothin

Components

Beta-lactamase

Keywords

HYDROLASE/INHIBITOR / class C beta-lactamase / Escherichia coli / cephalothin / structural genomic / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / HYDROLASE / HYDROLASE-INHIBITOR complex

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 (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Chang, C. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: class C beta-lactamase from Escherichia coli in complex with Cephalothin
Authors: Chang, C. / Maltseva, N. / Endres, M. / Joachimiak, A.

History

Deposition	Apr 8, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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
Revision 1.2	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6whf.cif.gz	363.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6whf.ent.gz	245.3 KB	Display	PDB format
PDBx/mmJSON format	6whf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6whf_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	6whf_full_validation.pdf.gz	1.2 MB	Display
Data in XML	6whf_validation.xml.gz	31 KB	Display
Data in CIF	6whf_validation.cif.gz	45.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wh/6whf ftp://data.pdbj.org/pub/pdb/validation_reports/wh/6whf	HTTPS FTP

-
Related structure data

Related structure data	6wa7 PDB Unreleased entryS 6xfs S: Starting model for refinement
Similar structure data	4old-1 3gtc-2 3ixh-2 1my8-2 1xgj-2 1fco-2 1xgj-1 4jxw-1 6tzi-3 4e3n-1 3gvb-1 1ga9-1 1kvm-1 6t7l-d 4nk3-d 6tzg-4 3gr2-1 1ke0-1 6tpm-d 5waf-3 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: CSGID-IDP97257

-
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

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

1

A: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	155.185, 46.298, 108.854
Angle α, β, γ (deg.)	90.000, 116.580, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y

Components on special symmetry positions

ID	Model	Components
1	1	B-748- HOH
2	1	B-753- HOH

#1: Protein	Beta-lactamase Mass: 39658.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: class C beta-lactamase / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: A35218R Gene: bla(ampc-EC31), blaEC, AJ318_17250, AZZ83_002790, D7Y10_20755, D7Y10_27165, D9L99_20655, D9L99_27090, DJ487_18405, DW236_18485, ELT23_15185 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q104Z6, UniProt: P00811*PLUS, beta-lactamase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-9EP / (2R)-5-[(acetyloxy)methyl]-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / Cephalotin, bound form Mass: 398.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₁₈N₂O₆S₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.38 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 10% 2-propanol, 20% PEG4000

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97918 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 19, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.4→50 Å / Num. obs: 133142 / % possible obs: 97.5 % / Redundancy: 6.3 % / B_iso Wilson estimate: 16.43 Å² / R_merge(I) obs: 0.076 / R_pim(I) all: 0.033 / R_rim(I) all: 0.083 / Χ²: 1.325 / Net I/σ(I): 11.7 / Num. measured all: 839925

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.4-1.42	6.3	0.334	6510	0.949	0.141	0.364	0.785	96.5
1.42-1.45	6.3	0.299	6594	0.957	0.126	0.325	0.822	96.3
1.45-1.48	6.3	0.264	6520	0.96	0.112	0.288	0.922	97.4
1.48-1.51	6.3	0.236	6601	0.966	0.1	0.256	1.005	97
1.51-1.54	6.2	0.209	6601	0.972	0.089	0.228	1.115	96.9
1.54-1.58	6	0.191	6533	0.972	0.083	0.209	1.26	95.9
1.58-1.62	6.3	0.17	6541	0.979	0.071	0.184	1.37	96.6
1.62-1.66	6.5	0.155	6618	0.983	0.065	0.169	1.472	97.1
1.66-1.71	6.5	0.144	6633	0.984	0.06	0.156	1.58	97.9
1.71-1.76	6.3	0.13	6731	0.985	0.055	0.142	1.739	98.5
1.76-1.83	6.3	0.119	6633	0.987	0.051	0.129	1.709	97.8
1.83-1.9	6	0.112	6488	0.986	0.049	0.123	1.653	95.6
1.9-1.99	6.5	0.1	6755	0.991	0.042	0.109	1.554	98.7
1.99-2.09	6.5	0.096	6736	0.991	0.04	0.104	1.437	98.8
2.09-2.22	6.4	0.089	6755	0.992	0.038	0.097	1.288	98.7
2.22-2.39	6.1	0.085	6610	0.991	0.037	0.093	1.239	96.9
2.39-2.63	6.5	0.079	6786	0.993	0.033	0.086	1.304	98.8
2.63-3.02	6.4	0.074	6846	0.994	0.031	0.08	1.258	99.5
3.02-3.8	6.1	0.068	6704	0.994	0.03	0.075	1.352	97
3.8-50	6.2	0.061	6947	0.992	0.027	0.067	1.589	97.8

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
PHENIX	1.17.1_3660	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6wa7

6wa7
PDB Unreleased entry

Resolution: 1.4→48.67 Å / SU ML: 0.1206 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.9979
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1807	12903	4.99 %
R_work	0.163	-	-
obs	0.1638	133136	96.57 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.36 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→48.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5610	0	88	425	6123

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0057	5999
X-RAY DIFFRACTION	f_angle_d	0.8704	8199
X-RAY DIFFRACTION	f_chiral_restr	0.0811	884
X-RAY DIFFRACTION	f_plane_restr	0.0057	1064
X-RAY DIFFRACTION	f_dihedral_angle_d	13.9735	2203

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 (%)
1.4-1.41	0.2718	382	0.2168	7273	X-RAY DIFFRACTION	85.81
1.41-1.43	0.212	419	0.2002	8043	X-RAY DIFFRACTION	95.72
1.43-1.45	0.216	516	0.1979	8130	X-RAY DIFFRACTION	95.45
1.45-1.47	0.2135	461	0.1917	8140	X-RAY DIFFRACTION	97.08
1.47-1.49	0.1966	425	0.1839	8166	X-RAY DIFFRACTION	95.61
1.49-1.51	0.2061	435	0.1759	8176	X-RAY DIFFRACTION	96.67
1.51-1.53	0.1869	474	0.1695	8173	X-RAY DIFFRACTION	96.89
1.53-1.55	0.1857	395	0.1627	8185	X-RAY DIFFRACTION	96.05
1.55-1.57	0.2001	439	0.1667	8021	X-RAY DIFFRACTION	95.1
1.57-1.6	0.1802	487	0.1581	8088	X-RAY DIFFRACTION	94.69
1.6-1.63	0.1838	397	0.159	8231	X-RAY DIFFRACTION	98.15
1.63-1.66	0.2112	403	0.1577	8224	X-RAY DIFFRACTION	96.07
1.66-1.69	0.1815	427	0.1558	8296	X-RAY DIFFRACTION	97.77
1.69-1.72	0.1964	420	0.1574	8245	X-RAY DIFFRACTION	96.93
1.72-1.76	0.1554	402	0.1513	8406	X-RAY DIFFRACTION	98.23
1.76-1.8	0.1781	403	0.1588	8204	X-RAY DIFFRACTION	96.83
1.8-1.85	0.1745	380	0.1596	8264	X-RAY DIFFRACTION	96.67
1.85-1.9	0.2015	444	0.1629	7980	X-RAY DIFFRACTION	94.64
1.9-1.95	0.1836	412	0.1612	8299	X-RAY DIFFRACTION	97.72
1.95-2.02	0.1782	452	0.1626	8300	X-RAY DIFFRACTION	97.21
2.02-2.09	0.1756	426	0.1636	8352	X-RAY DIFFRACTION	98.58
2.09-2.17	0.1829	472	0.1635	8258	X-RAY DIFFRACTION	98.22
2.17-2.27	0.1906	449	0.1614	8348	X-RAY DIFFRACTION	98.35
2.27-2.39	0.1832	395	0.1682	8134	X-RAY DIFFRACTION	95.53
2.39-2.54	0.1739	427	0.1645	8365	X-RAY DIFFRACTION	98.44
2.54-2.74	0.1795	444	0.1756	8429	X-RAY DIFFRACTION	98.86
2.74-3.01	0.1937	429	0.1749	8356	X-RAY DIFFRACTION	98.85
3.01-3.45	0.1853	425	0.1721	8191	X-RAY DIFFRACTION	96.55
3.45-4.34	0.172	436	0.1508	8299	X-RAY DIFFRACTION	97.52
4.34-48.67	0.1546	427	0.1464	8243	X-RAY DIFFRACTION	97

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	0.253116794927	0.17503524487	-0.00123080140912	0.395369604785	0.0318159152339	0.0320736455643	-0.137785848818	0.362070684608	0.0988020059486	-0.517543739709	0.066984099839	0.0631054110632	-0.548426215358	-0.100497284389	-0.0135597090507	0.364019834917	0.0840273360419	-0.0961729364564	0.226212020211	0.0534242830339	0.182472119451	24.2451695374	14.2936756997	13.7914937754
2	0.231557603777	0.143515375959	0.236433879356	0.547175411761	0.163692047048	0.267000263408	-0.0137135675675	0.0421947052279	-0.0233628347022	-0.0717414843792	-0.0461752301703	0.128887182151	-0.0701436687595	-0.197804919398	-0.0280533649806	0.127281202665	0.0149275951938	-0.0156599090035	0.177538118003	-0.0421214194156	0.132768955216	21.2490869668	0.672774806677	21.4583815562
3	0.536162790472	-0.0073165087872	0.15937893119	0.602447025797	0.00448600407686	0.214234587033	0.0215418051524	-0.0870120992395	-0.0892769131683	0.221478292364	-0.00817981713082	-0.0861080959389	0.140440530399	-0.0335023923595	-0.00411665939401	0.209724507764	-0.0244762348793	-0.0238882709376	0.115546867063	0.00969049643785	0.133863448572	36.481997557	-10.8957831706	44.308408784
4	0.278952538345	0.16639318306	-0.007966436662	0.470137667775	0.0398669335689	0.740322236559	0.0107183103219	0.0531314823142	-0.084113103361	-0.018839801369	-0.0385006412899	0.129044532215	0.16899721077	-0.171119791397	-0.0194804823804	0.109659909216	-0.0334278853724	-0.00478488749985	0.145457313331	-0.0416918412091	0.129516092642	20.9378941646	-7.93234653285	27.7147303908
5	0.495305719053	-0.0284382491454	0.226909197372	0.648265035031	0.0237266424421	0.828131853131	-0.037139375938	-0.000537313618047	0.0634476867342	0.0449907287936	-0.054121672429	0.0451774767975	-0.0956008393938	-0.0928994875823	-0.192853956341	0.100458882441	0.0012102358961	-0.00254114442058	0.0911928895759	-0.0254013600715	0.1153340752	28.4880304311	8.4601479677	33.8982126298
6	0.108022259058	-0.0129046550655	0.00373046220721	0.107163024696	-0.0839386363968	0.193000592446	0.0130032232933	0.164066366731	-0.188538143981	-0.443433250323	-0.0522205582655	0.0495982275816	0.533942272083	-0.0360507658609	0.0109432194179	0.457918812379	0.0129981807412	0.0528393493184	0.186741482621	-0.011977212692	0.225338860804	67.48247805	-9.80710242984	4.05455222059
7	0.826025695238	0.132917807752	-0.535596046399	0.511203873833	-0.222460702157	0.345147423708	0.0157915591241	0.0188126255032	0.0969050462272	-0.197277141999	-0.00336445408651	-0.140746003875	0.105279641758	0.0316821320177	0.0065491775404	0.186440301264	0.00408810302539	0.0259555572011	0.149913959728	0.0311100864699	0.137596048368	69.0904567435	5.27452078051	9.23853736573
8	0.470000272346	-0.0693606963562	-0.490941323978	0.614435063597	-0.0994861652209	0.487706916164	0.0919241790056	-0.142476043043	0.176585644616	0.0972886425282	0.0626463796641	0.0917280276351	-0.195512917499	0.212046207482	0.0527078321112	0.172312722332	-0.0406947353236	0.0334379051811	0.152444208837	-0.0290232690099	0.193246075165	56.3203729119	17.5108567373	33.4909651744
9	0.64961894074	0.0231775135614	-0.648853062399	0.730733662566	-0.0499419978776	0.847549786546	0.12256160275	-0.111248423552	0.258175883158	-0.215914994616	0.0415381729344	-0.220499058771	-0.160563784933	0.164661979303	0.0878111083556	0.141167850627	-0.0410881455321	0.0315787534919	0.180870075447	-0.00261188626226	0.210698404331	70.8315007714	13.8206267753	16.7052525791
10	0.58133493183	0.00193778125642	-0.613401652329	0.631755040231	0.124541562876	0.716438521457	-0.115792849614	-0.11169777498	-0.0839812305338	-0.0551313798608	0.0229203906918	-0.0387802896193	0.175542190631	0.102753624573	-0.124634271352	0.126463058663	0.0064626945797	0.00436410541809	0.132139949834	0.0399797867367	0.127384315155	63.9310484862	-3.07372966854	23.3548767309

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 30 through 50 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 51 through 106 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 107 through 189 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 190 through 265 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 266 through 388 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 30 through 50 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 51 through 106 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 107 through 189 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 190 through 282 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 283 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