PDB-4j72: Crystal Structure of polyprenyl-phosphate N-acetyl hexosamine 1-p...

ID or keywords:

Entry

Database: PDB / ID: 4j72

Title

Crystal Structure of polyprenyl-phosphate N-acetyl hexosamine 1-phosphate transferase

Components

Phospho-N-acetylmuramoyl-pentapeptide-transferase

Keywords

TRANSFERASE / Alpha-helical membrane protein / membrane enzyme / magnesium binding / undecaprenyl phosphate binding / UDP-MurNAc-pentapeptide binding / membrane

Function / homology

Function and homology information

phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / cell wall macromolecule biosynthetic process / phosphotransferase activity, for other substituted phosphate groups / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division ...
Similarity search - Function

Biological species

Aquifex aeolicus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.3 Å

Authors

Lee, S.Y. / Chung, B.C. / Gillespie, R.A. / Kwon, D.Y. / Guan, Z. / Zhou, P. / Hong, J.

Citation

Journal: Science / Year: 2013
Title: Crystal structure of MraY, an essential membrane enzyme for bacterial cell wall synthesis.
Authors: Chung, B.C. / Zhao, J. / Gillespie, R.A. / Kwon, D.Y. / Guan, Z. / Hong, J. / Zhou, P. / Lee, S.Y.

History

Deposition	Feb 12, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4j72.cif.gz	251.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4j72.ent.gz	205.9 KB	Display	PDB format
PDBx/mmJSON format	4j72.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4j72_validation.pdf.gz	448.5 KB	Display	wwPDB validaton report
Full document	4j72_full_validation.pdf.gz	462.5 KB	Display
Data in XML	4j72_validation.xml.gz	23.5 KB	Display
Data in CIF	4j72_validation.cif.gz	31.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j7/4j72 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/4j72	HTTPS FTP

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Related structure data

Similar structure data	6oyz-1 6oz6-2 6oyh-2 4gp4-d 30043 4g7s-d 5i56-d 5jnq-1 5ndc-d 3s8g-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phospho-N-acetylmuramoyl-pentapeptide-transferase

B: Phospho-N-acetylmuramoyl-pentapeptide-transferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	95.799, 101.491, 138.313
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-MurNAc-pentapeptide phosphotransferase Mass: 40954.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_053, mraY / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) References: UniProt: O66465, phospho-N-acetylmuramoyl-pentapeptide-transferase
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.1 Å³/Da / Density % sol: 70.03 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 20-120 mM magnesium acetate, 9 mM nickel chloride, 50 mM sodium cacodylate, pH 5.6, 45% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-BM / Wavelength: 0.9753 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 7, 2012

Radiation

Monochromator: liquid nitrogen cooled double crystal Si(220)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9753 Å / Relative weight: 1

Reflection

Resolution: 3.3→49.08 Å / Num. all: 20991 / Num. obs: 20890 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 6.5 % / R_merge(I) obs: 0.071 / R_sym value: 0.071 / Net I/σ(I): 35.98

Reflection shell

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
3.3-3.36	3.6	2	0.467	1	97.3
3.36-3.42	4.2	2.5	0.415	1	98.7
3.42-3.48	5	3.2	0.394	1	99.8
3.48-3.55	5.6	4.1	0.35	1	99.7
3.55-3.63	6.2	5.4	0.301	1	99.9
3.63-3.72	6.4	6.8	0.252	1	100
3.72-3.81	6.5	8.1	0.22	1	99.9
3.81-3.91	6.5	10.5	0.177	1	99.9
3.91-4.03	6.9	16	0.135	1	100
4.03-4.16	7	19.7	0.119	1	99.9
4.16-4.31	7	23	0.111	1	99.9
4.31-4.48	7.2	28.3	0.098	1	100
4.48-4.68	7.3	36.8	0.079	1	100
4.68-4.93	7.3	42.5	0.069	1	100
4.93-5.24	7.3	41	0.073	1	100
5.24-5.64	7.3	40.6	0.069	1	100
5.64-6.21	7.3	43.2	0.068	1	99.9
6.21-7.1	7.4	51.3	0.072	1	100
7.1-8.94	7.4	66.4	0.059	1	99.8
8.94-50	6.9	67.8	0.047	1	96.1

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SHELXD		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 3.3→26.689 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 25.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2649	1930	9.88 %
R_work	0.2227	-	-
obs	0.2269	19537	93.76 %
all	-	19537	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.3→26.689 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4761	0	4	5	4770

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4890
X-RAY DIFFRACTION	f_angle_d	1.193	6679
X-RAY DIFFRACTION	f_dihedral_angle_d	14.253	1609
X-RAY DIFFRACTION	f_chiral_restr	0.053	825
X-RAY DIFFRACTION	f_plane_restr	0.007	790

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 (%)
3.3-3.4177	0.3249	124	0.2679	1106	X-RAY DIFFRACTION	60
3.4177-3.5543	0.2601	156	0.2372	1497	X-RAY DIFFRACTION	81
3.5543-3.7156	0.2599	207	0.2237	1790	X-RAY DIFFRACTION	97
3.7156-3.9109	0.2664	196	0.207	1849	X-RAY DIFFRACTION	100
3.9109-4.1551	0.2413	207	0.1914	1850	X-RAY DIFFRACTION	100
4.1551-4.4746	0.2579	210	0.2059	1853	X-RAY DIFFRACTION	100
4.4746-4.9223	0.2586	197	0.1966	1892	X-RAY DIFFRACTION	100
4.9223-5.6288	0.2506	212	0.2255	1894	X-RAY DIFFRACTION	100
5.6288-7.0698	0.3086	205	0.2578	1900	X-RAY DIFFRACTION	100
7.0698-26.6899	0.2694	216	0.2534	1976	X-RAY DIFFRACTION	99

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	1.3156	0.996	-0.9489	1.5966	0.2596	1.8038	-0.1855	-0.9426	-0.9784	1.1101	0.0204	-0.3642	0.9703	0.2805	0.2108	0.6656	-0.0323	0.0388	0.676	0.4185	0.4237	103.4671	98.1187	154.878
2	3.3074	-0.1916	0.0965	3.0831	-0.1002	3.1618	0.0534	-0.9053	0.0026	1.0574	-0.0949	0.4986	0.1053	-0.4333	0.0395	0.5793	-0.016	0.0865	0.7132	-0.1464	0.0558	97.3783	114.9503	158.6346
3	2.0018	-2.5465	2.1299	5.8937	-0.9583	3.9868	0.0235	-0.7724	0.3955	0.9642	-0.1044	0.7341	-0.8606	-0.5085	0.1634	0.5796	-0.0456	-0.0081	0.4159	-0.3886	0.5864	101.4424	131.4008	154.7214
4	4.2875	1.2816	-1.1775	2.0749	-2.1351	4.7823	0.1386	0.2413	0.1972	-0.0058	-0.0245	-0.5815	0.3001	1.0884	-0.1145	0.199	0.0645	-0.0716	0.273	0.0491	0.5509	119.6344	124.5493	139.5987
5	0.4647	0.553	0.226	1.3676	-0.4007	1.1087	-0.0388	-0.2792	0.4398	0.4043	0.1491	0.0006	-0.1487	-0.1309	-0.079	0.1609	0.0277	0.0161	0.1555	-0.0699	0.1759	102.8391	120.8138	143.7269
6	4.9262	-0.0466	1.2578	3.0929	0.6551	1.9296	-0.199	0.1366	-0.2099	0.209	0.1058	-0.5985	0.0316	0.2347	0.1191	0.2338	-0.0086	-0.0434	0.2609	0.1305	0.2977	110.2939	108.6055	145.6029
7	3.2785	0.9979	0.5067	3.975	0.4868	3.4456	0.1529	-0.5542	-0.2142	0.4302	-0.3016	0.7028	-0.0393	-0.867	0.1406	0.2063	0.0549	0.2001	0.4743	0.0494	0.3795	94.8996	116.3417	148.2671
8	2.1248	-0.7147	-0.0226	1.8478	0.302	0.6484	0.0735	-0.0567	0.2171	-0.0267	0.0359	0.6619	0.086	-0.0084	-0.1028	0.1466	-0.0394	0.0247	0.2732	0.0698	0.3371	92.1135	121.7212	135.2731
9	9.3447	-1.2352	1.2346	1.4552	-0.4125	1.6121	0.0514	1.8892	0.4311	-1.1126	-0.153	-0.2568	-0.925	0.4245	0.0221	0.9419	-0.0285	0.0627	0.542	-0.0815	0.2147	104.5722	108.0045	121.9785
10	3.4729	0.3217	2.0747	4.813	1.0995	9.8215	0.1206	0.0666	0.0117	-0.493	-0.1265	0.8771	0.0693	-1.7672	0.1739	1.2306	-0.161	-0.0155	1.1963	-0.4633	0.1997	95.2301	98.2623	118.0367
11	1.9911	0.0238	-0.1577	2.3143	0.0387	1.4432	0.4431	0.0488	-0.5573	-0.4495	-0.0131	0.4704	0.8178	-0.4096	-0.1753	1.3758	-0.2668	-0.0005	0.7913	-1.175	1.2729	96.3828	80.942	120.4053
12	1.0623	-0.5135	0.1188	4.0874	0.1988	3.2622	-0.1331	0.1861	-1.4459	-0.4625	0.0882	-0.0048	1.1446	-0.0148	-0.0424	0.7047	-0.0148	0.1006	0.3194	-0.2172	1.0316	103.0913	88.6284	131.8889
13	0.8939	-0.0012	0.0026	2.2334	0.3524	2.2603	0.1147	-0.0758	-1.3434	0.0997	0.0122	0.342	1.2699	-0.5905	-0.0395	0.7516	-0.1776	0.0326	0.402	0.149	0.9838	92.7628	87.0243	142.4972

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 39 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 123 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 124 through 149 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 150 through 170 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 171 through 217 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 218 through 254 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 255 through 281 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 282 through 357 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 14 through 39 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 40 through 97 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 98 through 149 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 150 through 284 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 285 through 357 )

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