PDB-5zj1: Crystal structure of NDM-1 in complex with D-captopril derivative...

ID or keywords:

Entry

Database: PDB / ID: 5zj1

Title

Crystal structure of NDM-1 in complex with D-captopril derivative CYT-14

Components

Metallo-beta-lactamase type 2

Keywords

HYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / inhibitor / thio compounds

Function / homology

Function and homology information

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

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 0.96 Å

Authors

Zhang, H. / Hao, Q.

Funding support

China, 1items

Citation

Journal: to be published
Title: Crystal structure of NDM-1
Authors: Zhang, H. / Hao, Q.

History

Deposition	Mar 18, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 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	5zj1.cif.gz	111.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5zj1.ent.gz	82.4 KB	Display	PDB format
PDBx/mmJSON format	5zj1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5zj1_validation.pdf.gz	755.3 KB	Display	wwPDB validaton report
Full document	5zj1_full_validation.pdf.gz	755.4 KB	Display
Data in XML	5zj1_validation.xml.gz	13.5 KB	Display
Data in CIF	5zj1_validation.cif.gz	20.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zj/5zj1 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/5zj1	HTTPS FTP

-
Related structure data

Related structure data	5zj7C 5zj8C 5zjcC 3q6x PDB Unreleased entryS 5zio S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4tzf-d 6d1e-d 5ypi-6 6d1d-d 6fy5-1 5wig-1 6d1a-d 1dr6-d 6v1m-d 6d1g-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	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (4) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Metallo-beta-lactamase type 2

hetero molecules

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

1

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

Unit cell

Length a, b, c (Å)	41.449, 59.944, 41.964
Angle α, β, γ (deg.)	90.00, 98.42, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1 Mass: 25631.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pRHisMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C7C422, beta-lactamase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-YT4 / methyl (2R)-2-(phenylmethoxycarbonylamino)-3-sulfanyl-propanoate Mass: 269.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₁₅NO₄S
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.01 Å³/Da / Density % sol: 38.87 % / Mosaicity: 0.23 ° / Mosaicity esd: 0.004 °
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris pH5.5, 15% PEG 3350, 20mM L-proline

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U1 / Wavelength: 0.98 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 0.96→50 Å / Num. obs: 117982 / % possible obs: 95.3 % / Redundancy: 5.7 % / B_iso Wilson estimate: 18.25 Å² / R_merge(I) obs: 0.068 / Χ²: 0.952 / Net I/σ(I): 21.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
0.96-0.99	3.3	0.351	7812	1.174	1	63.5
0.99-1.03	4.1	0.202	11272	1.005	1	91.1
1.03-1.08	4.6	0.125	12300	0.835	1	100
1.08-1.14	4.7	0.089	12348	0.945	1	99.9
1.14-1.21	4.7	0.076	12342	0.891	1	99.9
1.21-1.3	4.7	0.065	12347	0.779	1	100
1.3-1.43	4.8	0.061	12372	0.744	1	100
1.43-1.64	7.8	0.089	12346	1.136	1	99.9
1.64-2.07	9.3	0.072	12336	1.003	1	99.2
2.07-50	7.6	0.061	12507	0.945	1	99.5

-
Processing

Software

Name	Version	Classification
PHENIX	dev_1992	refinement
DENZO		data reduction
SCALEPACK		data scaling
PDB_EXTRACT	3.24	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3Q6X

3q6x
PDB Unreleased entry

Resolution: 0.96→27.936 Å / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.25 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1499	5114	5.02 %
R_work	0.1312	-	-
obs	0.132	101936	82.55 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 0.96→27.936 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1702	0	40	252	1994

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	1877
X-RAY DIFFRACTION	f_angle_d	1.118	2557
X-RAY DIFFRACTION	f_dihedral_angle_d	12.773	689
X-RAY DIFFRACTION	f_chiral_restr	0.053	279
X-RAY DIFFRACTION	f_plane_restr	0.006	341

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 (%)
0.9602-0.9711		0	0.176	5	X-RAY DIFFRACTION	0.13
0.9711-0.9825	0.2083	3	0.1986	142	X-RAY DIFFRACTION	4
0.9825-0.9945	0.2337	28	0.1976	600	X-RAY DIFFRACTION	15
0.9945-1.0071	0.1441	66	0.1359	1310	X-RAY DIFFRACTION	34
1.0071-1.0203	0.1371	107	0.1259	1850	X-RAY DIFFRACTION	48
1.0203-1.0343	0.1178	117	0.1162	2372	X-RAY DIFFRACTION	61
1.0343-1.0491	0.1204	149	0.1039	2614	X-RAY DIFFRACTION	67
1.0491-1.0648	0.1203	149	0.1056	3064	X-RAY DIFFRACTION	79
1.0648-1.0814	0.118	181	0.1026	3387	X-RAY DIFFRACTION	87
1.0814-1.0991	0.1055	198	0.1074	3560	X-RAY DIFFRACTION	91
1.0991-1.1181	0.1256	214	0.1044	3735	X-RAY DIFFRACTION	96
1.1181-1.1384	0.1105	207	0.1016	3843	X-RAY DIFFRACTION	98
1.1384-1.1603	0.1222	209	0.1053	3898	X-RAY DIFFRACTION	100
1.1603-1.184	0.1248	223	0.1086	3839	X-RAY DIFFRACTION	100
1.184-1.2097	0.1178	203	0.1084	3918	X-RAY DIFFRACTION	100
1.2097-1.2379	0.1369	189	0.1104	3909	X-RAY DIFFRACTION	100
1.2379-1.2688	0.1373	238	0.1082	3875	X-RAY DIFFRACTION	100
1.2688-1.3031	0.1321	202	0.1117	3912	X-RAY DIFFRACTION	100
1.3031-1.3415	0.1209	200	0.1121	3897	X-RAY DIFFRACTION	100
1.3415-1.3848	0.1295	210	0.1135	3911	X-RAY DIFFRACTION	100
1.3848-1.4343	0.13	173	0.1195	3946	X-RAY DIFFRACTION	100
1.4343-1.4917	0.1326	201	0.116	3901	X-RAY DIFFRACTION	100
1.4917-1.5596	0.1328	195	0.1172	3925	X-RAY DIFFRACTION	100
1.5596-1.6418	0.131	233	0.1203	3861	X-RAY DIFFRACTION	100
1.6418-1.7447	0.142	221	0.1278	3913	X-RAY DIFFRACTION	100
1.7447-1.8793	0.1506	192	0.13	3918	X-RAY DIFFRACTION	99
1.8793-2.0684	0.1417	212	0.1274	3841	X-RAY DIFFRACTION	99
2.0684-2.3676	0.1353	211	0.1352	3929	X-RAY DIFFRACTION	100
2.3676-2.9824	0.1662	199	0.1425	3970	X-RAY DIFFRACTION	100
2.9824-27.9474	0.1659	184	0.1366	3977	X-RAY DIFFRACTION	99

-
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