PDB-7u35: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate lig...

ID or keywords:

Entry

Database: PDB / ID: 7u35

Title

Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with ADP

Components

UDP-N-acetylmuramoylalanine--D-glutamate ligase

Keywords

LIGASE / SSGCID / UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase / MurD / ADP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

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 / cytoplasm
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with ADP
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Feb 25, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7u35.cif.gz	608.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7u35.ent.gz	416.8 KB	Display	PDB format
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Validation report

Summary document	7u35_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	7u35_full_validation.pdf.gz	2.3 MB	Display
Data in XML	7u35_validation.xml.gz	53 KB	Display
Data in CIF	7u35_validation.cif.gz	78.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u3/7u35 ftp://data.pdbj.org/pub/pdb/validation_reports/u3/7u35	HTTPS FTP

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Related structure data

Related structure data	7sy9S S: Starting model for refinement
Similar structure data	5a5e-d 5uq1-2 4arj-1 6uxc-d 5uq2-d 3bh7-d 4ise-d 5ulm-1 2ixu-d 4p5x-d Search similar-shape structures by Omokage search (details) 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

Related structure data

7sy9S

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

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

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

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

hetero molecules

146 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

hetero molecules

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

2

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

hetero molecules

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

3

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

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.190, 131.180, 79.540
Angle α, β, γ (deg.)	90.000, 106.931, 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

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and ((resid 8 through 10 and (name N...
d_2	ens_1	(chain "B" and ((resid 8 through 10 and (name N...
d_3	ens_1	(chain "C" and (resid 8 through 16 or (resid 17...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	HIS	ARG	A	1 - 32
d_1	2	ens_1	PRO	THR	A	35 - 117
d_1	3	ens_1	LEU	ASP	A	119 - 165
d_1	4	ens_1	LEU	ILE	A	167 - 251
d_1	5	ens_1	GLY	ARG	A	253 - 295
d_1	6	ens_1	ARG	VAL	A	297 - 300
d_1	7	ens_1	TYR	ARG	A	302 - 346
d_1	8	ens_1	PRO	LEU	A	348 - 358
d_1	9	ens_1	GLY	GLY	A	360
d_1	10	ens_1	ASP	PRO	A	362 - 375
d_1	11	ens_1	VAL	VAL	A	377
d_1	12	ens_1	VAL	PHE	A	379 - 411
d_1	13	ens_1	ASN	ALA	A	413 - 429
d_1	14	ens_1	ADP	ADP	B
d_1	15	ens_1	EDO	EDO	C
d_2	1	ens_1	HIS	ARG	D	2 - 33
d_2	2	ens_1	PRO	THR	D	36 - 118
d_2	3	ens_1	LEU	ASP	D	120 - 166
d_2	4	ens_1	LEU	GLU	D	168 - 180
d_2	5	ens_1	HIS	ILE	D	188 - 259
d_2	6	ens_1	GLY	ARG	D	261 - 303
d_2	7	ens_1	ARG	VAL	D	305 - 308
d_2	8	ens_1	TYR	ARG	D	310 - 354
d_2	9	ens_1	PRO	LEU	D	356 - 366
d_2	10	ens_1	GLY	GLY	D	368
d_2	11	ens_1	ASP	PRO	D	370 - 383
d_2	12	ens_1	VAL	VAL	D	385
d_2	13	ens_1	VAL	PHE	D	387 - 419
d_2	14	ens_1	ASN	ALA	D	421 - 437
d_2	15	ens_1	ADP	ADP	E
d_2	16	ens_1	EDO	EDO	F
d_3	1	ens_1	HIS	THR	G	1 - 115
d_3	2	ens_1	LEU	ASP	G	117 - 163
d_3	3	ens_1	LEU	ILE	G	165 - 249
d_3	4	ens_1	GLY	ARG	G	251 - 293
d_3	5	ens_1	ARG	VAL	G	295 - 298
d_3	6	ens_1	TYR	ARG	G	300 - 344
d_3	7	ens_1	PRO	LEU	G	346 - 356
d_3	8	ens_1	GLY	GLY	G	358
d_3	9	ens_1	ASP	PRO	G	360 - 373
d_3	10	ens_1	VAL	VAL	G	375
d_3	11	ens_1	VAL	PHE	G	377 - 409
d_3	12	ens_1	ASN	ALA	G	411 - 427
d_3	13	ens_1	ADP	ADP	H
d_3	14	ens_1	EDO	EDO	I

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.997719455426, 0.0240425678347, 0.0630701450475), (-0.0527888333541, -0.304349731405, 0.951096514591), (0.0420621841743, -0.952256895972, -0.302386469169)	38.6898280739, 11.950690659, 135.532196967
2	given	(0.993691269325, 0.0869560504966, -0.070825888971), (-0.00826574350581, -0.573024700319, -0.819496412627), (-0.111845155241, 0.814911859103, -0.568690885405)	20.4788623392, 140.881106884, 42.5290292558

#1: Protein	UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase Mass: 48312.270 Da / Num. of mol.: 3 / Fragment: PsaeA.17938.a.B2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: murD, PA4414 / Plasmid: PsaeA.17938.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9HVZ9, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 868 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.8 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.55 Details: Optimization condition around RigakuReagents JCSG Top96 B6: 21% (w/V) PEG 3350, 100mM HEPES/NaOH pH 7.55: PsaeA.17938.a.B2.PW38065 at 40mg/ml + 5mM ADP + 5mM MgCl2. Tray: 324078 e4: cryo: ...Details: Optimization condition around RigakuReagents JCSG Top96 B6: 21% (w/V) PEG 3350, 100mM HEPES/NaOH pH 7.55: PsaeA.17938.a.B2.PW38065 at 40mg/ml + 5mM ADP + 5mM MgCl2. Tray: 324078 e4: cryo: 20% EG + compounds in 2 steps: puck ECC9-7.

Crystal

Density Matthews: 2.35 Å³/Da / Density % sol: 47.8 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.55
Details: Optimization condition around RigakuReagents JCSG Top96 B6: 21% (w/V) PEG 3350, 100mM HEPES/NaOH pH 7.55: PsaeA.17938.a.B2.PW38065 at 40mg/ml + 5mM ADP + 5mM MgCl2. Tray: 324078 e4: cryo: ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 17, 2022

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.95→50 Å / Num. obs: 95481 / % possible obs: 98.2 % / Redundancy: 5.111 % / B_iso Wilson estimate: 37.332 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.044 / R_rim(I) all: 0.049 / Χ²: 0.96 / Net I/σ(I): 21.07

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.95-2	4.704	0.314	4.28	6920	0.931	0.353	96.4
2-2.06	5.185	0.255	5.72	6827	0.964	0.283	97.3
2.06-2.12	5.206	0.209	7.12	6571	0.973	0.232	97.4
2.12-2.18	5.194	0.168	8.81	6451	0.983	0.187	97.9
2.18-2.25	5.202	0.129	11.24	6275	0.989	0.143	97.8
2.25-2.33	5.193	0.11	13.12	6100	0.992	0.122	98.1
2.33-2.42	5.178	0.094	15.14	5856	0.993	0.104	98.1
2.42-2.52	5.203	0.083	17.14	5676	0.994	0.092	98.2
2.52-2.63	5.163	0.072	19.3	5424	0.996	0.08	98.3
2.63-2.76	5.167	0.06	23	5208	0.997	0.067	98.7
2.76-2.91	5.146	0.053	26.15	4942	0.997	0.059	98.6
2.91-3.08	5.13	0.044	30.08	4722	0.998	0.049	98.9
3.08-3.3	5.105	0.038	34.7	4430	0.998	0.043	99.1
3.3-3.56	5.078	0.035	38.28	4123	0.999	0.039	99
3.56-3.9	5.042	0.032	40.98	3790	0.999	0.036	99.1
3.9-4.36	5.035	0.03	43.4	3455	0.999	0.033	99.4
4.36-5.03	5.045	0.029	44.67	3060	0.999	0.032	99.3
5.03-6.17	5.038	0.029	43.89	2587	0.999	0.033	99
6.17-8.72	4.979	0.028	45.09	2005	0.999	0.031	99.2
8.72-50	4.823	0.027	46.91	1059	0.999	0.03	94.1

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.20-4438	refinement
PDB_EXTRACT	3.27	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: apo structure, pdb entry 7SY9, in two domains

7sy9

Resolution: 1.95→37.91 Å / SU ML: 0.1995 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3586
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2045	2000	2.09 %	0
R_work	0.1705	93469	-	-
obs	0.1713	95469	98.25 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 41.58 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→37.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9456	0	93	868	10417

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0067	9799
X-RAY DIFFRACTION	f_angle_d	0.8496	13344
X-RAY DIFFRACTION	f_chiral_restr	0.0564	1569
X-RAY DIFFRACTION	f_plane_restr	0.0074	1787
X-RAY DIFFRACTION	f_dihedral_angle_d	11.2624	3526

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	1.15328917006
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	1.21093972772

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 (%)
1.95-2	0.2436	127	0.2105	6527	X-RAY DIFFRACTION	96.3
2-2.05	0.2467	141	0.1991	6588	X-RAY DIFFRACTION	97.38
2.05-2.11	0.2526	149	0.1915	6577	X-RAY DIFFRACTION	97.49
2.11-2.18	0.2172	165	0.1812	6604	X-RAY DIFFRACTION	97.93
2.18-2.26	0.2282	123	0.1753	6689	X-RAY DIFFRACTION	97.86
2.26-2.35	0.2134	154	0.1749	6646	X-RAY DIFFRACTION	98.19
2.35-2.46	0.2357	128	0.1819	6659	X-RAY DIFFRACTION	98.25
2.46-2.59	0.2339	132	0.186	6707	X-RAY DIFFRACTION	98.43
2.59-2.75	0.2046	133	0.1849	6729	X-RAY DIFFRACTION	98.65
2.75-2.96	0.2229	151	0.1868	6711	X-RAY DIFFRACTION	98.83
2.96-3.26	0.2385	140	0.1801	6721	X-RAY DIFFRACTION	99.08
3.26-3.73	0.1825	141	0.1659	6723	X-RAY DIFFRACTION	99.05
3.73-4.7	0.1717	151	0.1452	6803	X-RAY DIFFRACTION	99.36
4.7-37.91	0.1879	165	0.1587	6785	X-RAY DIFFRACTION	98.67

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	2.30161806321	-0.647437758391	-0.654013075043	8.38989463642	-1.79293142666	2.62204080595	0.108015216244	0.0264296870024	-0.794070854979	0.194705407832	-0.450203808088	-0.0453103128739	0.222931090392	0.117004771529	0.286571675784	0.366318502267	0.0425862327772	0.00828869811228	0.284527899045	-0.0453714653295	0.600046235648	-34.7985057057	44.9892263352	39.2071907017
2	2.22385512762	-0.192820023531	-0.0454095042852	2.58451847613	0.228268267183	2.05343318461	0.107366263057	0.0222901877343	0.00997493131307	-0.205763483976	-0.0445578310571	-0.191627706696	-0.231133417163	0.114526530054	-0.0627063376109	0.251575750381	-0.0107665562815	0.0231600529196	0.143197546396	0.0272003757972	0.150227063157	-40.4811080843	72.8991901766	41.2228867597
3	1.29963250845	-0.15795310306	0.46364361649	1.33612541066	-0.0924322179892	3.13242466256	0.0135811925988	-0.312647971404	-0.00600641746533	-0.000511197111614	0.0564721124276	0.0544301227269	0.0255909417613	-0.204508662028	-0.0722610054814	0.134000193133	-0.00915731033705	-0.00856379359685	0.211587448588	0.0170945009866	0.210374244435	-48.0977965182	74.4245216951	63.4443641174
4	4.83344664216	1.13783127029	1.72633031574	5.16341005418	-0.490603529863	5.09618026396	0.254191398167	-0.756901228926	0.276162241988	0.520883610793	-0.113405751464	-0.616415270135	-0.776221364119	0.12794683276	-0.137176425445	0.391541748349	-0.0901699239376	0.0286242646575	0.396726150658	-0.0266983640642	0.329747004476	7.87871940744	36.4629744745	80.4104942334
5	1.97135469575	-0.415208116563	0.0846939507825	2.12023576013	-0.47107059914	3.52563922833	0.119787486956	0.0514050121978	-0.00274194576233	-0.23253175134	0.00118273984958	0.0466909202924	0.229002577028	0.0280718401738	-0.105962562044	0.307991353003	0.0244028873286	-0.00572983727304	0.136826282394	0.0057401239825	0.190981993184	0.250960619189	32.7433778506	49.4072814873
6	2.28348153101	0.753318138213	-0.562289619911	3.05159055835	-0.882983584026	1.96224488557	0.0645072214632	0.050746643289	0.33060842073	0.343762532417	0.18589028762	0.65537716633	-0.362554747449	-0.244571074852	-0.174097201051	0.384161266708	0.089948050455	0.0480215441205	0.190658648422	0.0529085466468	0.318664205531	-2.093870304	59.0594185704	42.6728557122
7	0.691821982143	0.499117439403	0.550076099887	1.26569337584	0.0550248521051	0.638723220802	-0.376511605177	1.51871885898	1.2055661266	-0.811740312227	-0.138748013683	-0.306770252816	-0.632071932103	1.27304850095	0.171488965797	0.402404601082	-0.442594318759	-0.226357084985	1.46067632893	0.773801338585	1.02292284944	-12.3955153362	84.0988631252	61.2878646507
8	2.50643271281	0.471458186068	1.04803493903	3.32354286917	-0.347680140646	2.12979690397	-0.0826223015052	0.203872481899	0.389680103472	0.116499482716	-0.13335067177	-0.114454418711	-0.168437521169	0.406573282781	0.118846131018	0.142890683177	-0.025503247084	-0.0221926143825	0.392915154731	0.0666534067599	0.299996405974	-15.386127399	68.4953071901	80.0188884684
9	1.02935207845	0.114586759127	0.080266623471	3.06317945569	1.10804552806	1.94264195109	0.104336031712	-0.0365261167778	-0.00347626856652	0.262766091027	-0.188761951803	0.164906720736	0.265483171177	-0.242579491064	0.0715491834688	0.170571769641	-0.0135896451931	-0.000691174704495	0.356539785378	0.0399897585259	0.233986548064	-25.0899496994	50.9263408267	82.4838417191
10	3.1570511817	-0.273401570783	-0.811885882753	4.82983406765	0.0819129684247	2.8549795104	0.00862658840929	0.68022073373	-0.206785305953	-0.742350541345	-0.182638523389	0.266923362217	0.252916134081	-0.488752771256	0.122207899866	0.360340660598	0.0271923625448	-0.0625528419802	0.462564687407	-0.0108497019944	0.213935810087	-24.6757296789	40.4686266807	64.8328573835

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 8 through 106 )	A	A	8 - 106	1 - 99
2	2	chain 'A' and (resid 107 through 257 )	A	A	107 - 257	100 - 238
3	3	chain 'A' and (resid 258 through 448 )	A	A	258 - 448	239 - 429
4	4	chain 'B' and (resid 7 through 106 )	B	D	7 - 106	1 - 100
5	5	chain 'B' and (resid 107 through 310 )	B	D	107 - 310	101 - 299
6	6	chain 'B' and (resid 311 through 448 )	B	D	311 - 448	300 - 437
7	7	chain 'C' and (resid 8 through 106 )	C	G	8 - 106	1 - 97
8	8	chain 'C' and (resid 107 through 234 )	C	G	107 - 234	98 - 213
9	9	chain 'C' and (resid 235 through 361 )	C	G	235 - 361	214 - 340
10	10	chain 'C' and (resid 362 through 448 )	C	G	362 - 448	341 - 427

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