PDB-6xv5: Crystal structure of penicillin-binding protein 2 from Yersinia p...

ID or keywords:

Entry

Database: PDB / ID: 6xv5

Title

Crystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with ertapenem

Components

Peptidoglycan D,D-transpeptidase MrdA

Keywords

MEMBRANE PROTEIN / Class B PBP /

Yersinia pestis / HMM transpeptidase /

periplasmic protein / peptidoglycan crosslinking /

ertapenem

Function / homology

Function and homology information

serine-type D-Ala-D-Ala carboxypeptidase /

serine-type D-Ala-D-Ala carboxypeptidase activity /

penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape /

proteolysis /

plasma membrane
Similarity search - Function

Biological species

Yersinia pestis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.673 Å

Authors

Pankov, G. / Hunter, W.N. / Dawson, A.

Citation

Journal: To Be Published
Title: The structure of penicillin-binding protein 2 from Yersinia pestis
Authors: Pankov, G.

History

Deposition	Jan 21, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 3, 2021	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6xv5.cif.gz	229.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6xv5.ent.gz		Display	PDB format
PDBx/mmJSON format	6xv5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6xv5_validation.pdf.gz	341.7 KB	Display	wwPDB validaton report
Full document	6xv5_full_validation.pdf.gz	357.6 KB	Display
Data in XML	6xv5_validation.xml.gz	40.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xv/6xv5 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/6xv5	HTTPS FTP

-
Related structure data

Related structure data	6tiiSC 6tix S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6vw9-1 6tix-2 3a18-2 3a16-2 3a17-3 3a17-2 5okg-2 3ela-d 3a18-1 5ogt-1 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	#29 - May 2002 Penicillin-binding Proteins similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

BBB: Peptidoglycan D,D-transpeptidase MrdA

AAA: Peptidoglycan D,D-transpeptidase MrdA

hetero molecules

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

1

BBB: Peptidoglycan D,D-transpeptidase MrdA

defined by author
Evidence: native gel electrophoresis
66 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

AAA: Peptidoglycan D,D-transpeptidase MrdA

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.265, 147.772, 164.523
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain: (Details: Chains BBB AAA)

#1: Protein	Peptidoglycan D,D-transpeptidase MrdA / Penicillin-binding protein 2 / PBP-2 Mass: 66012.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: mrdA, YPO2604 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A384KFW3, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.49 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion Details: Crystals were grown in a condition containing 1 uL of 1 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM ertapenem) and 2 uL of reservoir solution (0.5 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5).

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.67→109.937 Å / Num. obs: 38541 / % possible obs: 100 % / Redundancy: 13.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.133 / Net I/σ(I): 12.2
Reflection shell	Resolution: 2.701→7.331 Å / R_merge(I) obs: 0.04 / Num. unique obs: 2108 / CC_1/2: 0.999

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
STARANISO		data scaling
PHASES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6TII

6tii

Resolution: 2.673→109.937 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.883 / SU B: 18.456 / SU ML: 0.351 / Cross valid method: FREE R-VALUE / ESU R Free: 0.461

	R_factor	Num. reflection	% reflection
R_free	0.2851	1485	4.834 %
R_work	0.213	-	-
all	0.216	-	-
obs	-	30718	77.249 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 77.799 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.278 Å²	0 Å²	0 Å²
2-	-	0.125 Å²	0 Å²
3-	-	-	-0.402 Å²

Refinement step

Cycle: LAST / Resolution: 2.673→109.937 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8499	0	10	149	8658

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.013	8758
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	8142
X-RAY DIFFRACTION	r_angle_refined_deg	1.279	1.656	11898
X-RAY DIFFRACTION	r_angle_other_deg	1.102	1.578	18881
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.792	5	1072
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.947	21.5	460
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.737	15	1468
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.948	15	65
X-RAY DIFFRACTION	r_chiral_restr	0.053	0.2	1140
X-RAY DIFFRACTION	r_chiral_restr_other	0.118	0.2	2
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	9797
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1866
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	1802
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	7914
X-RAY DIFFRACTION	r_nbtor_refined	0.158	0.2	4107
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	3946
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	281
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.077	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.187	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.244	0.2	84
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.069	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	3.194	8.218	4288
X-RAY DIFFRACTION	r_mcbond_other	3.191	8.217	4286
X-RAY DIFFRACTION	r_mcangle_it	5.381	12.314	5357
X-RAY DIFFRACTION	r_mcangle_other	5.38	12.314	5357
X-RAY DIFFRACTION	r_scbond_it	2.658	8.594	4470
X-RAY DIFFRACTION	r_scbond_other	2.659	8.592	4467
X-RAY DIFFRACTION	r_scangle_it	4.707	12.745	6540
X-RAY DIFFRACTION	r_scangle_other	4.707	12.744	6539
X-RAY DIFFRACTION	r_lrange_it	8.551	94.13	9693
X-RAY DIFFRACTION	r_lrange_other	8.51	94.127	9679
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.112	0.05	16451

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.673-2.742	0.486	15	0.413	154	0.42	2851	0.669	0.697	5.9277	0.42
2.742-2.817	0.269	25	0.362	600	0.358	2866	0.635	0.697	21.8074	0.356
2.817-2.899	0.4	47	0.33	946	0.333	2703	0.733	0.772	36.737	0.326
2.899-2.988	0.339	69	0.293	1509	0.295	2685	0.788	0.823	58.771	0.28
2.988-3.086	0.353	96	0.285	1826	0.288	2582	0.792	0.812	74.4384	0.27
3.086-3.194	0.331	106	0.294	1959	0.296	2491	0.799	0.809	82.8984	0.276
3.194-3.314	0.323	99	0.286	2162	0.288	2476	0.835	0.828	91.3166	0.266
3.314-3.45	0.329	116	0.27	2180	0.273	2296	0.85	0.857	100	0.241
3.45-3.603	0.311	109	0.254	2138	0.257	2247	0.843	0.888	100	0.228
3.603-3.778	0.307	89	0.227	2075	0.23	2164	0.882	0.91	100	0.204
3.778-3.983	0.266	114	0.206	1946	0.209	2060	0.908	0.932	100	0.189
3.983-4.224	0.233	106	0.194	1839	0.196	1945	0.932	0.94	100	0.176
4.224-4.515	0.246	75	0.177	1757	0.18	1832	0.921	0.945	100	0.163
4.515-4.876	0.289	98	0.175	1614	0.181	1712	0.905	0.946	100	0.166
4.876-5.34	0.28	69	0.185	1517	0.189	1586	0.939	0.947	100	0.174
5.34-5.969	0.303	80	0.191	1368	0.196	1448	0.906	0.947	100	0.182
5.969-6.889	0.304	43	0.183	1261	0.187	1304	0.923	0.949	100	0.18
6.889-8.429	0.252	50	0.177	1048	0.18	1098	0.923	0.954	100	0.185
8.429-11.885	0.203	48	0.153	833	0.156	882	0.956	0.973	99.8866	0.171
11.885-109.937	0.374	31	0.305	501	0.308	537	0.877	0.903	99.0689	0.341

-
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