PDB-8cp9: 1,6-anhydro-n-actetylmuramic acid kinase (AnmK)in complex with no...

ID or keywords:

Entry

Database: PDB / ID: 8cp9

Title

1,6-anhydro-n-actetylmuramic acid kinase (AnmK)in complex with non-hydrolyzable AMPPNP.

Components

Anhydro-N-acetylmuramic acid kinase

Keywords

TRANSFERASE / Anhydro-sugar kinase Phosphotransferase ATP binding

Function / homology

Function and homology information

anhydro-N-acetylmuramic acid kinase / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover / kinase activity / phosphorylation / response to antibiotic / ATP binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Jimenez-Faraco, E. / Hermoso, J.A.

Funding support

Spain, 1items

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Catalytic process of anhydro-N-acetylmuramic acid kinase from Pseudomonas aeruginosa.
Authors: El-Araby, A.M. / Jimenez-Faraco, E. / Feltzer, R. / Martin-Garcia, J.M. / Karri, B.R. / Ramachandran, B. / Kim, C. / Fisher, J.F. / Hermoso, J.A. / Mobashery, S.

History

Deposition	Mar 2, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 20, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8cp9.cif.gz	367.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8cp9_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8cp9_full_validation.pdf.gz	1.7 MB	Display
Data in XML	8cp9_validation.xml.gz	27.7 KB	Display
Data in CIF	8cp9_validation.cif.gz	38.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cp/8cp9 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/8cp9	HTTPS FTP

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Related structure data

Related structure data	8breC 8c0uC 8cpbC 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	#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: Anhydro-N-acetylmuramic acid kinase

B: Anhydro-N-acetylmuramic acid kinase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: equilibrium centrifugation, sedimentation velocity analytical ultracentrifugation (SV-AUC)

Unit cell

Length a, b, c (Å)	89.940, 89.940, 176.958
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃

#1: Protein	Anhydro-N-acetylmuramic acid kinase / AnhMurNAc kinase Mass: 39473.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GAGAG expresion tag in N-terminal. These five aminoacids should be renumbered from -4 to 0. Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: anmK, PA0666 / Production host: Escherichia coli (E. coli) References: UniProt: Q9I5Q5, anhydro-N-acetylmuramic acid kinase
#2: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.62 Å³/Da / Density % sol: 54.32 % / Description: Hexagonal crystals
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, Na/K tartrate 0.2M

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALBA

/ Beamline: XALOC / Wavelength: 0.97926 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97926 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.5356
pseudo-merohedral	2	2	-K, -H, -L	2	0.4644

Reflection

Resolution: 2.2→47.024 Å / Num. obs: 41089 / % possible obs: 100 % / Redundancy: 20.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.099 / Net I/σ(I): 21

Reflection shell

Resolution: 2.2→2.27 Å / Redundancy: 21.3 % / R_merge(I) obs: 1.717 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3557 / CC_1/2: 0.701 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS	v0.86	data reduction
Aimless	0.7.9	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→47.024 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.951 / WR_factor R_free: 0.212 / WR_factor R_work: 0.172 / SU B: 8.792 / SU ML: 0.126 / Average fsc free: 0.9577 / Average fsc work: 0.9763 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.231	2042	4.975 %
R_work	0.1833	39006	-
all	0.186	-	-
obs	-	41048	99.981 %

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: 53.71 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.845 Å²	0 Å²	0 Å²
2-	-	0.845 Å²	0 Å²
3-	-	-	-1.69 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→47.024 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5401	0	64	123	5588

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	5594
X-RAY DIFFRACTION	r_bond_other_d	0.015	0.016	5054
X-RAY DIFFRACTION	r_angle_refined_deg	1.159	1.625	7626
X-RAY DIFFRACTION	r_angle_other_deg	0.64	1.552	11750
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.277	5	709
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.784	5	49
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.519	10	847
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.294	10	248
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	836
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6509
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1097
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	1268
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	4833
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	2712
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	2991
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.177	0.2	207
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.008	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.042	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.166	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.236	0.2	41
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.236	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	3.387	4.951	2847
X-RAY DIFFRACTION	r_mcbond_other	3.385	4.951	2847
X-RAY DIFFRACTION	r_mcangle_it	4.822	7.417	3551
X-RAY DIFFRACTION	r_mcangle_other	4.822	7.417	3552
X-RAY DIFFRACTION	r_scbond_it	3.276	5.25	2747
X-RAY DIFFRACTION	r_scbond_other	3.275	5.25	2747
X-RAY DIFFRACTION	r_scangle_it	4.69	7.77	4075
X-RAY DIFFRACTION	r_scangle_other	4.69	7.77	4076
X-RAY DIFFRACTION	r_lrange_it	6.944	64.498	6245
X-RAY DIFFRACTION	r_lrange_other	6.932	64.366	6235

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 (%)
2.2-2.257	0.48	169	0.394	2872	X-RAY DIFFRACTION	99.9014
2.257-2.319	0.366	147	0.303	2795	X-RAY DIFFRACTION	100
2.319-2.386	0.404	160	0.263	2712	X-RAY DIFFRACTION	100
2.386-2.459	0.314	134	0.221	2639	X-RAY DIFFRACTION	100
2.459-2.54	0.321	139	0.216	2563	X-RAY DIFFRACTION	100
2.54-2.629	0.3	111	0.189	2509	X-RAY DIFFRACTION	100
2.629-2.728	0.264	104	0.182	2420	X-RAY DIFFRACTION	100
2.728-2.84	0.275	134	0.195	2306	X-RAY DIFFRACTION	100
2.84-2.966	0.259	143	0.178	2178	X-RAY DIFFRACTION	100
2.966-3.11	0.238	98	0.196	2132	X-RAY DIFFRACTION	100
3.11-3.278	0.207	107	0.196	2004	X-RAY DIFFRACTION	100
3.278-3.477	0.272	82	0.19	1944	X-RAY DIFFRACTION	100
3.477-3.716	0.255	93	0.203	1782	X-RAY DIFFRACTION	100
3.716-4.014	0.196	120	0.18	1629	X-RAY DIFFRACTION	100
4.014-4.396	0.195	68	0.153	1548	X-RAY DIFFRACTION	100
4.396-4.913	0.159	68	0.137	1402	X-RAY DIFFRACTION	100
4.913-5.67	0.228	68	0.171	1236	X-RAY DIFFRACTION	99.9234
5.67-6.937	0.142	34	0.164	1062	X-RAY DIFFRACTION	100
6.937-9.781	0.153	40	0.133	814	X-RAY DIFFRACTION	100
9.781-47.024	0.155	23	0.152	459	X-RAY DIFFRACTION	99.177

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	0.2614	-0.0274	0.0117	0.3599	-0.1404	0.2822	-0.0011	-0.003	0.0134	-0.117	-0.0113	0.0061	0.0309	0.0347	0.0124	0.0516	-0.0042	0.0182	0.0225	-0.024	0.0545	13.2817	-18.287	-1.4109
2	0.4507	-0.0696	0.2708	0.0704	-0.0132	0.2123	-0.0282	-0.1231	-0.0004	0.0233	0.0103	0.0479	-0.0177	-0.043	0.0179	0.0408	0.0007	0.0447	0.0711	-0.0083	0.0651	22.8217	-24.2172	38.6282

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|1-363 }	A	1 - 363
2	X-RAY DIFFRACTION	2	{ B\|1-363 }	B	1 - 363

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