PDB-6bm9: Directed evolutionary changes in MBL super family - VIM-2 Round 10

ID or keywords:

Entry

Database: PDB / ID: 6bm9

Title

Directed evolutionary changes in MBL super family - VIM-2 Round 10

Components

Metallo-beta-lactamase

Keywords

HYDROLASE / Phosphatase / Directed evolution / MBL super family / NDM-1

Function / homology

Function and homology information

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

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.19 Å

Authors

Hong, N.-S. / Jackson, C.J. / Carr, P.D.

Citation

Journal: Elife / Year: 2019
Title: Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes.
Authors: Baier, F. / Hong, N. / Yang, G. / Pabis, A. / Miton, C.M. / Barrozo, A. / Carr, P.D. / Kamerlin, S.C. / Jackson, C.J. / Tokuriki, N.

History

Deposition	Nov 13, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 20, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3	Oct 4, 2023	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.pdbx_dist_value / _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

-
Download

PDBx/mmCIF format	6bm9.cif.gz	359.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6bm9.ent.gz	293.3 KB	Display	PDB format
PDBx/mmJSON format	6bm9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bm/6bm9 ftp://data.pdbj.org/pub/pdb/validation_reports/bm/6bm9	HTTPS FTP

-
Related structure data

Related structure data	1ko3S S: Starting model for refinement
Similar structure data	2bg8-d 3s8k-d 1sxr-d 2bfz-d 6fy5-d 2bga-d 1bhq-d 2a6v-d 2p72-d 5z7j-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Metallo-beta-lactamase

B: Metallo-beta-lactamase

C: Metallo-beta-lactamase

D: Metallo-beta-lactamase

hetero molecules

104 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Metallo-beta-lactamase

B: Metallo-beta-lactamase

hetero molecules

defined by author&software
Evidence: gel filtration
52 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Metallo-beta-lactamase

D: Metallo-beta-lactamase

hetero molecules

defined by author&software
52 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	128.596, 41.672, 156.764
Angle α, β, γ (deg.)	90.00, 99.41, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Metallo-beta-lactamase / VIM2R10 Mass: 25881.879 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: Q5U7L7
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 195 / 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 Å³/Da / Density % sol: 38.54 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES (pH 7.5), 1.2 M Sodium Citrate, 0.5 mM TCEP, 1.25 mM PNPP, 25 mM HEPES, 75 mM NaCl, 100 uM ZnCl2

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.19→37.14 Å / Num. obs: 41962 / % possible obs: 97.75 % / Redundancy: 3.6 % / B_iso Wilson estimate: 32.54 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.09382 / R_pim(I) all: 0.05747 / R_rim(I) all: 0.1103 / Net I/σ(I): 11.28
Reflection shell	Resolution: 2.19→2.268 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.7642 / Num. unique obs: 4019 / CC_1/2: 0.609 / R_pim(I) all: 0.4838 / R_rim(I) all: 0.9075 / % possible all: 95.73

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ko3

1ko3

Resolution: 2.19→37.892 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.11 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2672	2114	5.04 %
R_work	0.2211	-	-
obs	0.2234	41944	97.78 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.19→37.892 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6796	0	16	195	7007

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7022
X-RAY DIFFRACTION	f_angle_d	0.709	9603
X-RAY DIFFRACTION	f_dihedral_angle_d	12.154	2490
X-RAY DIFFRACTION	f_chiral_restr	0.024	1089
X-RAY DIFFRACTION	f_plane_restr	0.005	1262

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 (%)
2.19-2.241	0.3486	133	0.319	2563	X-RAY DIFFRACTION	96
2.241-2.297	0.345	139	0.3174	2559	X-RAY DIFFRACTION	96
2.297-2.3591	0.3692	111	0.3002	2630	X-RAY DIFFRACTION	97
2.3591-2.4285	0.3582	144	0.2849	2625	X-RAY DIFFRACTION	97
2.4285-2.5069	0.332	151	0.2793	2626	X-RAY DIFFRACTION	98
2.5069-2.5965	0.3451	143	0.2794	2655	X-RAY DIFFRACTION	98
2.5965-2.7004	0.3335	129	0.2713	2609	X-RAY DIFFRACTION	97
2.7004-2.8233	0.2796	149	0.2449	2640	X-RAY DIFFRACTION	98
2.8233-2.9721	0.2667	140	0.2396	2651	X-RAY DIFFRACTION	98
2.9721-3.1582	0.3055	156	0.237	2644	X-RAY DIFFRACTION	98
3.1582-3.4019	0.2581	146	0.2241	2691	X-RAY DIFFRACTION	99
3.4019-3.7439	0.2549	148	0.1957	2678	X-RAY DIFFRACTION	98
3.7439-4.2851	0.2404	142	0.1875	2690	X-RAY DIFFRACTION	98
4.2851-5.3962	0.1888	135	0.1703	2739	X-RAY DIFFRACTION	99
5.3962-37.898	0.2304	148	0.1844	2830	X-RAY DIFFRACTION	98

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	1.5219	0.787	1.0031	1.9664	-0.2863	4.3833	-0.0053	0.0657	-0.9884	-0.4503	0.0646	-0.411	0.4709	-0.5745	-0.0997	0.3419	-0.1219	0.0334	0.3652	-0.0777	0.4247	-25.1097	-8.1494	11.0367
2	3.0966	0.8046	-1.9241	2.978	1.225	3.6861	0.1399	0.3124	-0.3336	-0.0274	-0.0426	0.266	-0.1473	-0.799	-0.111	0.1707	-0.0095	0.0035	0.2495	0.0126	0.2702	-25.0407	-1.3812	18.3187
3	2.6301	-1.2478	0.4458	0.072	-0.1927	-0.4733	0.099	0.039	0.1197	-0.0252	-0.0559	-0.0404	-0.0331	-0.0334	-0.0593	0.3681	0.059	0.0319	0.3702	0.0163	0.3258	-36.9544	13.5871	17.6383
4	0.792	-0.2378	1.1796	1.6024	0.7011	3.7433	0.1459	0.1053	0.1811	-0.1051	-0.1325	-0.1358	-0.4237	0.4376	-0.0055	0.258	-0.0548	-0.0134	0.2224	0.0478	0.2196	-56.6267	24.1861	22.9824
5	1.1404	1.2471	-1.1469	2.7445	-1.2751	1.2016	-0.1232	-0.3916	-0.2394	0.7663	-0.757	-1.0102	0.1202	0.8527	0.4862	0.641	-0.1687	-0.1611	0.7476	0.2156	0.4514	-50.1608	18.9606	39.8989
6	2.5765	1.2024	1.1164	3.7816	0.2521	1.7632	0.1618	-0.6595	0.2426	0.9095	-0.3267	0.0124	-0.2627	-0.2445	0.1625	0.4405	-0.0165	-0.0141	0.4001	-0.005	0.2241	-59.037	23.5394	37.7907
7	1.5361	0.2107	-0.9766	4.4435	-0.1496	2.6252	0.2083	-0.2906	-0.4867	0.2984	-0.0286	0.0022	0.3873	0.3028	-0.1454	0.2904	0.0428	-0.0449	0.25	0.0941	0.3145	-55.2714	7.84	23.5345
8	2.2527	0.6276	0.0219	2.12	-1.2177	4.0997	0.1004	0.2146	0.1558	-0.038	0.0038	0.0523	-0.3232	-0.3524	-0.0466	0.1873	0.0778	0.0131	0.2138	0.0094	0.1873	-16.7756	9.375	9.2091
9	3.2421	-1.603	-0.5564	3.3986	1.4478	4.3733	0.1556	-0.6111	-0.8719	0.589	0.2718	-0.3952	0.9621	0.7557	-0.2931	0.4879	-0.0202	-0.0506	0.6077	0.1268	0.5375	8.8859	-24.1758	69.4839
10	3.5183	0.6115	-0.1522	-0.3739	0.2021	0.3736	0.121	-0.3769	-0.1103	-0.12	-0.0621	-0.0432	-0.1848	-0.0918	-0.0884	0.341	0.0451	0.0443	0.467	-0.0565	0.4114	17.5945	-13.6488	60.1992
11	2.4873	0.5815	1.1081	1.6406	-0.0202	2.8386	0.0764	-0.6187	0.1233	0.1163	-0.1488	0.5356	-0.5417	-0.3868	0.0322	0.3198	0.05	0.028	0.3418	-0.0694	0.351	41.3533	2.1193	53.6321
12	0.1911	0.5259	-0.5467	2.9953	-1.4375	2.4259	-0.4505	0.1902	0.6339	-0.1986	0.4216	0.9647	0.1367	-1.1149	-0.1059	0.4634	0.1709	-0.045	0.3234	-0.0856	0.4656	36.9496	-7.4105	38.1467
13	2.9601	-0.6973	0.6309	3.2451	-0.9833	2.7777	0.1818	0.0228	0.4203	-0.5991	-0.2643	-0.335	-0.1794	0.3925	0.0365	0.3371	-0.0441	0.0643	0.3132	-0.0553	0.2612	47.2099	-1.463	42.6507
14	2.3539	0.5744	0.9823	5.9813	-0.0281	4.6388	0.0184	0.4356	0.5458	-0.5303	-0.0431	0.4062	-0.049	0.1734	0.0558	0.4764	0.0149	0.0767	0.3722	-0.0498	0.3112	43.2914	-3.8369	34.2624
15	3.5038	0.0921	-0.2692	4.7527	0.3602	2.2898	0.3975	-0.405	-0.3702	0.1193	-0.3214	0.1886	0.4971	-0.3542	0.0611	0.3003	-0.0684	0.0218	0.445	0.0064	0.2684	41.7024	-15.6559	56.4692
16	0.378	-0.0953	-0.5209	4.0719	-0.7282	2.2852	0.7713	-0.5204	-0.3583	0.0348	-0.2407	0.9114	0.0226	-0.5687	-0.1272	0.2791	0.001	0.1403	0.7733	-0.0553	0.3916	35.344	-6.8535	59.1698
17	1.946	0.7856	0.899	3.001	1.1613	2.4983	-0.1085	0.6781	0.5034	-0.6142	0.5695	-0.6241	-0.7799	0.5048	-0.3633	0.4769	-0.0957	0.1005	0.4943	0.0652	0.513	9.8738	-9.1916	54.4065
18	2.9003	0.3215	1.387	1.8811	0.9981	2.3258	-0.1945	-0.4102	0.8394	-0.3367	-0.017	-0.1095	-0.6705	-0.252	0.3203	0.4383	0.0007	-0.0502	0.3811	-0.1183	0.5375	-0.6495	-9.4114	61.8778
19	0.1556	0.009	-0.0762	0.6214	-0.5892	0.598	0.2495	-0.8597	0.5148	0.8511	-0.0845	-0.4815	-0.1126	1.0936	-0.2146	0.9373	-0.1385	-0.04	1.0906	-0.2609	0.5988	6.3677	-7.4719	78.5993
20	2.3934	0.4362	0.5002	3.3026	0.037	1.8427	0.3111	-1.1354	0.58	0.2988	-0.5348	0.2351	-0.2397	-0.8416	0.2182	0.4748	0.0007	0.0425	0.7599	-0.1975	0.4922	-3.1826	-9.3952	76.6225

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 30 through 58 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 102 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 103 through 146 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 147 through 199 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 200 through 215 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 216 through 261 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 32 through 121 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 122 through 260 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 32 through 76 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 77 through 144 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 145 through 199 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 200 through 215 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 216 through 245 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 246 through 260 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 32 through 102 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 103 through 121 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 122 through 144 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 145 through 199 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 200 through 215 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 216 through 261 )

-
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