PDB-6rj7: Crystal structure of the 19F labelled OXA-48

ID or keywords:

Entry

Database: PDB / ID: 6rj7

Title

Crystal structure of the 19F labelled OXA-48

Components

Beta-lactamase

Keywords

ANTIMICROBIAL PROTEIN / beta lactmase / antibiotic resistance / 19F labelling

Function / homology

Function and homology information

penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73002235119 Å

Authors

Brem, J. / Lohans, C. / Schofield, C.

Funding support

United Kingdom, 1items

Citation

Journal: Chemistry / Year: 2019
Title: 19F NMR Monitoring of Reversible Protein Post-Translational Modifications: Class D beta-Lactamase Carbamylation and Inhibition.
Authors: van Groesen, E. / Lohans, C.T. / Brem, J. / Aertker, K.M.J. / Claridge, T.D.W. / Schofield, C.J.

History

Deposition	Apr 26, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 31, 2019	Provider: repository / Type: Initial release
Revision 1.1	Sep 25, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6rj7.cif.gz	357.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6rj7.ent.gz	242.3 KB	Display	PDB format
PDBx/mmJSON format	6rj7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6rj7_validation.pdf.gz	426.9 KB	Display	wwPDB validaton report
Full document	6rj7_full_validation.pdf.gz	427 KB	Display
Data in XML	6rj7_validation.xml.gz	22.6 KB	Display
Data in CIF	6rj7_validation.cif.gz	33.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rj/6rj7 ftp://data.pdbj.org/pub/pdb/validation_reports/rj/6rj7	HTTPS FTP

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Related structure data

Related structure data	4s2pS S: Starting model for refinement
Similar structure data	6goa-1 5dva-1 5dva-3 6pxx-d 5dtt-2 5dts-1 4wmc-2 6nlw-1 5dtt-4 5oe2-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, dimer

Unit cell

Length a, b, c (Å)	64.360, 58.030, 66.430
Angle α, β, γ (deg.)	90.000, 91.490, 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

#1: Protein	Beta-lactamase Mass: 28575.311 Da / Num. of mol.: 2 / Mutation: T213C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.38 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M CaCl2 0.1M Tris pH 8.0 20% w/v PEG6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 8, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9159 Å / Relative weight: 1
Reflection	Resolution: 1.73→66.4 Å / Num. obs: 51225 / % possible obs: 99.9 % / Redundancy: 16.8 % / B_iso Wilson estimate: 22.4197680721 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.137 / R_pim(I) all: 0.034 / R_rim(I) all: 0.141 / Net I/σ(I): 16.2
Reflection shell	Resolution: 1.73→1.76 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2576 / CC_1/2: 0.807 / R_pim(I) all: 0.455 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
PHENIX	1.11.1_2575	refinement
XDS		data reduction
XDS		data scaling
SHELXD		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4S2P

4s2p

Resolution: 1.73002235119→66.4 Å / SU ML: 0.206280929465 / Cross valid method: FREE R-VALUE / σ(F): 1.3475117612 / Phase error: 24.1930311135

	R_factor	Num. reflection	% reflection
R_free	0.209692980881	2465	4.81727574751 %
R_work	0.17738165197	-	-
obs	0.178951139219	51170	99.7446443539 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 31.0579600524 Å²

Refinement step

Cycle: LAST / Resolution: 1.73002235119→66.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3924	0	2	359	4285

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00804495180859	4055
X-RAY DIFFRACTION	f_angle_d	0.911123545479	5517
X-RAY DIFFRACTION	f_chiral_restr	0.0551173743125	583
X-RAY DIFFRACTION	f_plane_restr	0.00542749033517	712
X-RAY DIFFRACTION	f_dihedral_angle_d	18.7853042221	2367

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 (%)
1.73-1.7633	0.356880847054	124	0.312571399154	2724	X-RAY DIFFRACTION	99.6501049685
1.7633-1.7993	0.280980006036	140	0.2920510882	2672	X-RAY DIFFRACTION	99.7163120567
1.7993-1.8384	0.289757138784	138	0.26523846059	2707	X-RAY DIFFRACTION	99.649737303
1.8384-1.8812	0.282195902483	147	0.254379194379	2641	X-RAY DIFFRACTION	99.2524029904
1.8812-1.9282	0.271536692408	144	0.230531227367	2659	X-RAY DIFFRACTION	99.151043509
1.9282-1.9804	0.249794292693	119	0.204055677494	2680	X-RAY DIFFRACTION	99.5376955903
1.9804-2.0387	0.237951269953	144	0.19897583006	2701	X-RAY DIFFRACTION	99.8595998596
2.0387-2.1045	0.237057165492	113	0.190238519622	2723	X-RAY DIFFRACTION	99.8240056318
2.1045-2.1797	0.225893650573	113	0.184008453664	2706	X-RAY DIFFRACTION	99.6817538897
2.1797-2.267	0.247476801858	130	0.177356404662	2697	X-RAY DIFFRACTION	99.7529992943
2.267-2.3701	0.233077008153	146	0.185759173025	2697	X-RAY DIFFRACTION	100
2.3701-2.4951	0.206925585722	145	0.17393662953	2719	X-RAY DIFFRACTION	99.965095986
2.4951-2.6514	0.228018706946	159	0.173157827786	2683	X-RAY DIFFRACTION	99.8945518453
2.6514-2.8561	0.189778816244	165	0.171396556868	2687	X-RAY DIFFRACTION	99.9649491763
2.8561-3.1436	0.19163431385	128	0.179322842637	2736	X-RAY DIFFRACTION	99.965095986
3.1436-3.5984	0.1949383971	119	0.165965479336	2743	X-RAY DIFFRACTION	99.8256016742
3.5984-4.5335	0.166424250764	157	0.136087372891	2711	X-RAY DIFFRACTION	99.8259658893
4.5335-66.4565	0.192553871178	134	0.161255633785	2819	X-RAY DIFFRACTION	99.9323181049

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	2.98628347677	0.81962926633	-0.0410753568832	4.30582705331	0.438838427934	4.98920932537	-0.153857262029	-0.325215562222	0.503804780551	0.496989979248	0.0997172564854	-0.123951302976	-0.50496225448	-0.153273779542	-0.028095877893	0.352437023792	0.00112552299982	0.0385190283667	0.324015265308	-0.12566564917	0.396886119079	25.3159342691	30.6789677457	25.7243256904
2	3.42653264019	0.870244656111	0.478164569607	2.98783501191	0.541855658252	1.42014009194	-0.06483515911	-0.241447398462	0.617602868525	0.0250131629352	0.0452232501593	0.0515152113222	-0.25403560309	0.00926358671189	0.0350627701187	0.252961308813	0.00306226626629	0.0126600532761	0.214070804673	-0.0451821017597	0.226318459187	22.9755695145	28.4485392272	17.852263162
3	1.29234708907	0.0194397702403	0.338704961082	1.41616898995	-0.0555399475563	0.689461724231	0.0288604516747	0.0634407536081	-0.158899206695	-0.084166623671	0.031834076524	-0.155034056139	0.077891449355	0.035557569503	-0.0483720567763	0.179836522913	0.0110977523165	0.0218853628497	0.234490800307	-0.000839062398194	0.225377473325	31.4534960896	3.67176963578	9.97744105503
4	6.07835222372	0.466046213982	-0.699088139165	6.94045502289	0.672635907862	3.900030565	0.100429999317	0.810697076541	0.57133389344	-0.519301456357	-0.231381675202	-1.25723132481	-0.186429541648	0.605070246526	0.141536125528	0.278695103741	0.011140820879	0.109211035904	0.359160759918	0.086215866481	0.314987161568	37.0593849168	14.8404636334	4.33161529869
5	2.78802860629	0.410566894136	-0.802169979541	2.30230949416	0.242908431917	1.17262145575	0.123273398302	0.114644958454	0.253099254594	-0.0180011867308	-0.0803435950707	-0.331724223582	-0.072511191585	0.0966532855642	-0.0523056639883	0.189650509522	0.00601202894128	0.019960799902	0.225241030746	0.0364907888542	0.223173321208	29.5368898438	18.0978663448	9.2306146454
6	2.64614589463	0.775247991267	0.18142788673	1.76615750182	0.620901219037	1.36776890598	0.0225678665722	-0.0330638905636	-0.0425728636768	0.00798874851795	0.00742577013677	-0.120924688886	-0.038526620373	0.0591949458118	-0.0361439391683	0.16855990895	0.0274775980113	0.0114306844002	0.16650013939	0.0219869433901	0.154641427471	22.6951870753	14.2672373411	15.8847108401
7	6.61012229394	-1.65343447033	-0.114178591465	2.95827480102	0.338976194457	1.62867374543	-0.176582809135	-0.602055520867	0.151022909982	0.337439806955	0.127081053131	-0.082758785688	-0.0166813878053	0.0626664307341	0.0477128172311	0.261720705151	0.0072300752552	0.0146395816632	0.338913277313	-0.0164058883655	0.181653647248	21.5344768221	19.764017465	28.0664992298
8	1.84415692053	0.261405812702	-0.0494634270577	1.29005323738	-0.209530478567	0.828253349021	-0.039743973509	0.00711118885463	-0.180068076221	-0.00949858431895	0.0275685678939	0.00580698488132	0.113553670598	-0.00374467528803	0.0135484163715	0.138456721939	0.00254071973719	0.0164925752336	0.17162176503	-0.0165942184921	0.186935538998	-2.99386096498	-1.1750705684	15.668130938
9	0.995031629178	1.39477239865	0.165032113239	3.11774986216	-1.14361734672	1.69597776162	0.0181481611266	0.785759661454	-0.699669757758	-0.704053855125	0.0906173458076	0.981640433538	0.322657590689	-0.735850009371	-0.0700478161161	0.369299836437	-0.0642393186554	-0.0430621176097	0.447609834718	-0.063841698693	0.499462582103	-12.5689352664	-5.93780632357	7.6696447877
10	3.4385893325	0.69645119253	-0.282386627175	1.04325138333	-0.540900974731	1.39330215884	-0.0308182649618	-0.00525696297844	-0.192751134798	-0.0341260402066	-0.0153265042749	0.0150178012215	0.0545032255632	-0.092613110707	0.0615372784974	0.166184262074	0.026029121662	0.00339130704112	0.143645879827	-0.0193394944587	0.192690172678	1.03976728272	-3.49477755227	16.9316099878
11	8.04068569639	-0.899692125548	0.489825808106	3.36188518027	-0.839924366446	2.83131093997	-0.0585175424665	-1.00476478512	-0.184003807274	0.398827427824	-0.0965103301924	-0.117241698994	0.000482236476864	0.0720169578717	0.0924937780626	0.22841850645	0.00546069880471	0.0076497543784	0.331711305966	0.0706495116626	0.209008675	3.68769311547	-3.88036972494	31.5326954163

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 38 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 39 through 62 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 63 through 141 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 142 through 155 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 156 through 177 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 178 through 243 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 244 through 265 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 21 through 142 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 143 through 155 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 156 through 243 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 244 through 265 )

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