PDB-9dqw: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate lig...

ID or keywords:

Entry

Database: PDB / ID: 9dqw

Title

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and AMP-PNP

Components

UDP-N-acetylmuramoylalanine--D-glutamate ligase

Keywords

LIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / MurD

Function / homology

Function and homology information

UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / identical protein binding / cytoplasm
Similarity search - Function

Biological species

Escherichia coli K-12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and AMP-PNP
Authors: Seibold, S. / Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Sep 24, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9dqw.cif.gz	196.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9dqw.ent.gz	151.1 KB	Display	PDB format
PDBx/mmJSON format	9dqw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9dqw_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9dqw_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9dqw_validation.xml.gz	25.7 KB	Display
Data in CIF	9dqw_validation.cif.gz	37 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dq/9dqw ftp://data.pdbj.org/pub/pdb/validation_reports/dq/9dqw	HTTPS FTP

-
Related structure data

Similar structure data	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	#108 - Dec 2008 Hsp90 similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#108 - Dec 2008
Hsp90
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: UDP-N-acetylmuramoylalanine--D-glutamate ligase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	65.441, 65.441, 135.609
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

-
Protein , 1 types, 1 molecules A

#1: Protein	UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase Mass: 47949.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: murD, b0088, JW0086 / Plasmid: EscoA.17938.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase

#1: Protein

UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase

Mass: 47949.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli K-12 (bacteria) / Gene: murD, b0088, JW0086 / Plasmid: EscoA.17938.a.AE1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase

-
Non-polymers , 8 types, 427 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-UMA / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE Type: L-peptide linking / Mass: 750.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₃H₃₆N₄O₂₀P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H₂O

-
Details

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: 3.03 Å³/Da / Density % sol: 59.38 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.0 M ammonium sulfate, 0.1 Hepes pH 7.5, 7% (v/v) PEG 400. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Soaked with 5 mM AMP-PNP and UMA for 5 hours. plate Liu-S-097, A6. Puck: PSL-1616, Cryo: 2.5M ammonium sulfate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 24, 2024
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.45→47.09 Å / Num. obs: 100616 / % possible obs: 100 % / Redundancy: 12.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.025 / R_rim(I) all: 0.09 / Χ²: 1.01 / Net I/σ(I): 15.6 / Num. measured all: 1297494
Reflection shell	Resolution: 1.45→1.47 Å / % possible obs: 100 % / Redundancy: 13.2 % / R_merge(I) obs: 1.686 / Num. measured all: 65654 / Num. unique obs: 4968 / CC_1/2: 0.64 / R_pim(I) all: 0.478 / R_rim(I) all: 1.753 / Χ²: 1.05 / Net I/σ(I) obs: 1.7

-
Processing

Software

Name	Version	Classification
PHENIX	(dev_5462: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.45→47.09 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1647	4984	4.96 %
R_work	0.1498	-	-
obs	0.1505	100526	99.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.45→47.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3280	0	121	416	3817

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3532
X-RAY DIFFRACTION	f_angle_d	1.004	4825
X-RAY DIFFRACTION	f_dihedral_angle_d	15.873	1313
X-RAY DIFFRACTION	f_chiral_restr	0.081	556
X-RAY DIFFRACTION	f_plane_restr	0.01	621

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 (%)
1.45-1.47	0.2945	119	0.2651	3220	X-RAY DIFFRACTION	100
1.47-1.48	0.2655	180	0.2455	3159	X-RAY DIFFRACTION	100
1.48-1.5	0.2524	167	0.2297	3179	X-RAY DIFFRACTION	100
1.5-1.52	0.2302	187	0.216	3212	X-RAY DIFFRACTION	100
1.52-1.54	0.1985	184	0.2073	3103	X-RAY DIFFRACTION	100
1.54-1.56	0.207	183	0.192	3161	X-RAY DIFFRACTION	100
1.56-1.58	0.2063	171	0.1826	3170	X-RAY DIFFRACTION	100
1.58-1.61	0.2005	151	0.1756	3190	X-RAY DIFFRACTION	100
1.61-1.63	0.1818	161	0.1727	3180	X-RAY DIFFRACTION	100
1.63-1.66	0.201	163	0.1683	3184	X-RAY DIFFRACTION	100
1.66-1.69	0.1747	200	0.1665	3160	X-RAY DIFFRACTION	100
1.69-1.72	0.1862	148	0.1598	3189	X-RAY DIFFRACTION	100
1.72-1.75	0.1677	138	0.1609	3205	X-RAY DIFFRACTION	100
1.75-1.79	0.1743	180	0.1614	3169	X-RAY DIFFRACTION	100
1.79-1.83	0.1766	165	0.1593	3182	X-RAY DIFFRACTION	100
1.83-1.87	0.1626	161	0.1509	3182	X-RAY DIFFRACTION	100
1.87-1.92	0.1554	189	0.1402	3163	X-RAY DIFFRACTION	100
1.92-1.97	0.1666	155	0.1354	3179	X-RAY DIFFRACTION	100
1.97-2.03	0.1491	166	0.1355	3194	X-RAY DIFFRACTION	100
2.03-2.09	0.1646	167	0.1346	3174	X-RAY DIFFRACTION	100
2.09-2.17	0.1763	139	0.1366	3206	X-RAY DIFFRACTION	100
2.17-2.25	0.1499	190	0.137	3197	X-RAY DIFFRACTION	100
2.25-2.35	0.1643	134	0.1286	3208	X-RAY DIFFRACTION	100
2.36-2.48	0.1431	162	0.1298	3160	X-RAY DIFFRACTION	100
2.48-2.63	0.1503	169	0.1387	3205	X-RAY DIFFRACTION	100
2.63-2.84	0.1724	178	0.1482	3199	X-RAY DIFFRACTION	100
2.84-3.12	0.1675	172	0.1595	3180	X-RAY DIFFRACTION	100
3.12-3.57	0.1607	189	0.1467	3181	X-RAY DIFFRACTION	100
3.58-4.5	0.1288	146	0.1285	3213	X-RAY DIFFRACTION	100
4.51-47.09	0.1675	170	0.1606	3238	X-RAY DIFFRACTION	100

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	1.8403	-0.7074	0.8174	2.8101	0.4438	4.4508	-0.0355	-0.1005	0.0303	0.1717	0.2139	-0.3402	0.1646	0.3501	-0.1117	0.1418	0.034	-0.0223	0.1521	-0.0289	0.1883	39.6843	-25.2689	-13.5499
2	0.4533	-0.5291	-0.2192	2.1414	0.8955	0.8315	-0.0309	-0.0451	-0.026	0.1138	0.017	-0.0019	0.1255	0.0212	0.0047	0.1425	-0.0043	0.0044	0.1257	0.0081	0.1245	27.5547	-16.7641	-6.6878
3	0.5445	-0.2986	-0.0709	1.432	1.2375	3.6061	-0.0403	-0.0711	-0.0212	0.0639	-0.1046	0.2247	0.0914	-0.2954	0.1447	0.1182	-0.0161	-0.0031	0.1425	-0.021	0.1783	13.0336	-11.1589	-11.5112
4	3.5194	1.223	-0.0589	6.1962	2.5594	3.2775	0.0729	0.0451	0.2232	-0.1195	-0.1862	0.4702	-0.1894	-0.1213	0.0646	0.1484	0.0393	0.01	0.1322	-0.017	0.1513	12.102	9.3379	-0.4357
5	2.2468	0.0304	-0.3735	4.1793	-1.5755	2.1811	0.0242	-0.1163	0.0962	0.1955	0.0571	0.0181	-0.0335	-0.0244	-0.0764	0.1599	0.0267	0.0314	0.1439	-0.0332	0.1413	19.4544	3.4264	2.0108
6	1.5104	0.6509	0.335	2.6479	-0.021	1.1827	-0.0406	-0.0611	0.2141	-0.0105	0.02	0.2694	-0.1287	-0.0629	0.0195	0.1447	0.0061	0.0074	0.1091	-0.0067	0.176	25.1104	8.9189	-21.4107
7	7.6349	-2.2905	0.7248	5.3018	0.6082	4.3607	-0.0371	0.3928	-0.0418	-0.609	0.091	0.1616	0.0223	-0.1027	-0.0548	0.2571	-0.0494	-0.016	0.1543	0.0284	0.1156	26.6957	5.7772	-34.8392
8	1.6756	0.166	0.0827	5.0326	-0.5409	1.4583	-0.044	0.0722	-0.0539	-0.1445	-0.004	-0.3844	-0.0277	0.1288	0.0522	0.1509	-0.0196	0.0208	0.1455	-0.0081	0.1474	36.07	8.1407	-25.2341

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 58 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 172 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 173 through 226 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 227 through 265 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 266 through 295 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 296 through 363 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 364 through 389 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 390 through 439 )

-
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

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 8 types, 427 molecules

-
Details

-
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

-Protein , 1 types, 1 molecules A

-Non-polymers , 8 types, 427 molecules

-Details

-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

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 8 types, 427 molecules

-
Details

-
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