PDB-7mfn: N-Acetylmannosamine-6-phosphate 2-epimerase E180A from Staphyloco...

ID or keywords:

Entry

Database: PDB / ID: 7mfn

Title

N-Acetylmannosamine-6-phosphate 2-epimerase E180A from Staphylococcus aureus (strain MRSA USA300)

Components

N-acetylmannosamine-6-phosphate 2-epimerase

Keywords

ISOMERASE / Epimerase / NanE

Function / homology

Function and homology information

N-acylglucosamine-6-phosphate 2-epimerase / N-acetylmannosamine catabolic process / N-acylglucosamine-6-phosphate 2-epimerase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Currie, M.J. / Dobson, R.C.J.

Citation

Journal: J.Biol.Chem. / Year: 2021
Title: N-acetylmannosamine-6-phosphate 2-epimerase uses a novel substrate-assisted mechanism to catalyze amino sugar epimerization.
Authors: Currie, M.J. / Manjunath, L. / Horne, C.R. / Rendle, P.M. / Subramanian, R. / Friemann, R. / Fairbanks, A.J. / Muscroft-Taylor, A.C. / North, R.A. / Dobson, R.C.J.

History

Deposition	Apr 10, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 20, 2022	Group: Data collection / Database references / Category: citation / citation_author / diffrn_radiation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l
Revision 1.2	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	7mfn.cif.gz	126.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7mfn.ent.gz		Display	PDB format
PDBx/mmJSON format	7mfn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7mfn_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	7mfn_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7mfn_validation.xml.gz	26.5 KB	Display
Data in CIF	7mfn_validation.cif.gz	41 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mf/7mfn ftp://data.pdbj.org/pub/pdb/validation_reports/mf/7mfn	HTTPS FTP

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Related structure data

Related structure data	6vvaSC 7mfsC 7mqtC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

BBB: N-acetylmannosamine-6-phosphate 2-epimerase

AAA: N-acetylmannosamine-6-phosphate 2-epimerase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS

Unit cell

Length a, b, c (Å)	76.999, 174.446, 44.523
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	N-acetylmannosamine-6-phosphate 2-epimerase / ManNAc-6-P epimerase Mass: 24513.037 Da / Num. of mol.: 2 / Mutation: E180A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: nanE, BTN44_01590, EP54_02960, EQ90_08785, ERS072840_01491, FA040_00085, HMPREF3211_02501, NCTC10654_00351, NCTC10702_00560, NCTC7878_00328, RK64_02155 Production host: Escherichia coli (E. coli) References: UniProt: X5EM89, N-acylglucosamine-6-phosphate 2-epimerase
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 665 / 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: 3.04 Å³/Da / Density % sol: 59.57 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 1 M trisodium citrate, 0.1 M sodium cacodylate, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95366 Å / Relative weight: 1
Reflection	Resolution: 1.55→46.4 Å / Num. obs: 87948 / % possible obs: 99.5 % / Redundancy: 13.1 % / CC_1/2: 0.999 / Net I/σ(I): 13.5
Reflection shell	Resolution: 1.55→1.57 Å / Num. unique obs: 8254 / CC_1/2: 0.842

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6VVA

6vva

Resolution: 1.55→42.004 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.968 / SU B: 1.25 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1779	4414	5.019 %
R_work	0.1502	83534	-
all	0.152	-	-
obs	-	87948	99.449 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 19.856 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.244 Å²	0 Å²	-0 Å²
2-	-	0.147 Å²	0 Å²
3-	-	-	0.098 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→42.004 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3434	0	32	665	4131

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	3826
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3674
X-RAY DIFFRACTION	r_angle_refined_deg	1.905	1.64	5234
X-RAY DIFFRACTION	r_angle_other_deg	1.56	1.579	8527
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.282	5	511
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.925	23.687	179
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.332	15	693
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	29.585	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	531
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	4448
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	796
X-RAY DIFFRACTION	r_nbd_refined	0.244	0.2	798
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	3450
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	1864
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	1667
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.21	0.2	511
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.006	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.236	0.2	35
X-RAY DIFFRACTION	r_nbd_other	0.242	0.2	80
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.232	0.2	72
X-RAY DIFFRACTION	r_mcbond_it	1.716	1.792	1937
X-RAY DIFFRACTION	r_mcbond_other	1.693	1.79	1936
X-RAY DIFFRACTION	r_mcangle_it	2.395	2.689	2465
X-RAY DIFFRACTION	r_mcangle_other	2.398	2.69	2466
X-RAY DIFFRACTION	r_scbond_it	2.813	2.139	1888
X-RAY DIFFRACTION	r_scbond_other	2.812	2.141	1889
X-RAY DIFFRACTION	r_scangle_it	4.307	3.103	2761
X-RAY DIFFRACTION	r_scangle_other	4.306	3.104	2762
X-RAY DIFFRACTION	r_lrange_it	6.166	24.627	4559
X-RAY DIFFRACTION	r_lrange_other	6.166	24.626	4559

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
1.548-1.588	0.263	295	0.237	5726	0.238	6479	0.883	0.885	92.931	0.215
1.588-1.632	0.235	326	0.212	5905	0.213	6231	0.911	0.916	100	0.19
1.632-1.679	0.222	307	0.193	5814	0.195	6122	0.929	0.932	99.9837	0.169
1.679-1.73	0.237	311	0.19	5640	0.192	5951	0.92	0.936	100	0.165
1.73-1.787	0.216	290	0.169	5500	0.171	5791	0.939	0.947	99.9827	0.147
1.787-1.85	0.176	287	0.158	5283	0.159	5570	0.959	0.958	100	0.137
1.85-1.919	0.2	301	0.157	5090	0.159	5391	0.949	0.957	100	0.138
1.919-1.998	0.182	266	0.157	4931	0.159	5197	0.955	0.962	100	0.142
1.998-2.086	0.178	265	0.151	4723	0.152	4988	0.961	0.967	100	0.139
2.086-2.188	0.18	225	0.149	4545	0.15	4770	0.959	0.97	100	0.139
2.188-2.306	0.181	219	0.143	4351	0.144	4571	0.959	0.972	99.9781	0.136
2.306-2.445	0.168	207	0.144	4138	0.145	4345	0.964	0.969	100	0.139
2.445-2.613	0.154	171	0.135	3928	0.136	4099	0.972	0.974	100	0.134
2.613-2.822	0.167	189	0.138	3581	0.139	3770	0.967	0.974	100	0.141
2.822-3.09	0.174	168	0.149	3352	0.15	3520	0.965	0.969	100	0.158
3.09-3.452	0.168	156	0.14	3064	0.141	3220	0.97	0.976	100	0.154
3.452-3.982	0.143	145	0.126	2693	0.127	2838	0.978	0.981	100	0.146
3.982-4.866	0.14	122	0.121	2336	0.122	2458	0.981	0.984	100	0.143
4.866-6.835	0.191	103	0.168	1824	0.169	1927	0.973	0.976	100	0.196
6.835-42.004	0.221	61	0.18	1109	0.182	1173	0.965	0.969	99.7442	0.227

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