PDB-4c5n: Structure of the pyridoxal kinase from Staphylococcus aureus in c...

ID or keywords:

Entry

Database: PDB / ID: 4c5n

Title

Structure of the pyridoxal kinase from Staphylococcus aureus in complex with AMP-PCP and pyridoxal

Components

PHOSPHOMETHYLPYRIMIDINE KINASE

Keywords

TRANSFERASE / RIBOKINASE

Function / homology

Ribokinase / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-PXL / 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol / :

Function and homology information

Biological species

STAPHYLOCOCCUS AUREUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Nodwell, M. / Alte, F. / Sieber, S.A. / Schneider, S.

Citation

Journal: J.Am.Chem.Soc. / Year: 2014
Title: A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.
Authors: Nodwell, M.B. / Koch, M.F. / Alte, F. / Schneider, S. / Sieber, S.A.

History

Deposition	Sep 12, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Apr 16, 2014	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4c5n.cif.gz	415.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4c5n.ent.gz	343.7 KB	Display	PDB format
PDBx/mmJSON format	4c5n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4c5n_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	4c5n_full_validation.pdf.gz	2 MB	Display
Data in XML	4c5n_validation.xml.gz	44.9 KB	Display
Data in CIF	4c5n_validation.cif.gz	61.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c5/4c5n ftp://data.pdbj.org/pub/pdb/validation_reports/c5/4c5n	HTTPS FTP

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Related structure data

Related structure data	4c5jSC 4c5kC 4c5lC 4c5mC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4c5m-1 3ibq-2 4c5k-1 4c5j-1 1vi9-2 5ilg-d 2i5b-2 6k90-d 3zs7-1 1td2-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#118 - Oct 2009 Sodium-Potassium Pump similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: PHOSPHOMETHYLPYRIMIDINE KINASE

B: PHOSPHOMETHYLPYRIMIDINE KINASE

C: PHOSPHOMETHYLPYRIMIDINE KINASE

D: PHOSPHOMETHYLPYRIMIDINE KINASE

hetero molecules

123 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PHOSPHOMETHYLPYRIMIDINE KINASE

D: PHOSPHOMETHYLPYRIMIDINE KINASE

hetero molecules

defined by author&software
61.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: PHOSPHOMETHYLPYRIMIDINE KINASE

C: PHOSPHOMETHYLPYRIMIDINE KINASE

hetero molecules

defined by author&software
61.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	62.190, 100.660, 168.210
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.9986, 0.0088, -0.0515), (-0.0117, 0.9983, -0.0567), (0.0509, 0.0572, 0.9971)	4.5086, -1.3277, 43.351
2	given	(-0.9952, -0.0108, -0.0977), (0.0063, -0.9989, 0.0464), (-0.0981, 0.0455, 0.9941)	-35.3184, -0.5133, 40.3711
3	given	(-0.986, -0.007, -0.1665), (0.0072, -1, -0.0004), (-0.1665, -0.0016, 0.986)	-23.6436, -1.6405, -1.9464

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Protein , 1 types, 4 molecules ABCD

#1: Protein	PHOSPHOMETHYLPYRIMIDINE KINASE / PYRIDOXAL KINASE Mass: 29811.793 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: MU50 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: C8MK44, pyridoxal kinase

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Non-polymers , 5 types, 328 molecules

#2: Chemical	ChemComp-PXL / 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE / PYRIDOXAL Mass: 167.162 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₉NO₃
#3: Chemical	ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-UEG / 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol Mass: 169.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₁NO₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y
Sequence details	FIRST AMINOACID IS A GLY INSTEAD OF MET DUE TO REMOVAL OF THE AFFINITY TAG

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 45 % / Description: NONE
Crystal grow	Details: 50MM HEPES PH7.6, 2M NH4SO4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
Detector	Type: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 18, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.75→48.26 Å / Num. obs: 107272 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 8.8 % / R_merge(I) obs: 0.15 / Net I/σ(I): 12.6
Reflection shell	Resolution: 1.75→1.81 Å / Redundancy: 7.8 % / R_merge(I) obs: 1.5 / Mean I/σ(I) obs: 1 / % possible all: 98

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C5J

4c5j

Resolution: 1.75→48.26 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.923 / SU B: 6.545 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25333	5340	5 %	RANDOM
R_work	0.20427	-	-	-
obs	0.2067	101932	99.71 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 26.636 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.67 Å²	0 Å²	0 Å²
2-	-	-1.2 Å²	0 Å²
3-	-	-	-0.47 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→48.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8109	0	207	313	8629

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.02	8592
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8070
X-RAY DIFFRACTION	r_angle_refined_deg	1.938	1.993	11719
X-RAY DIFFRACTION	r_angle_other_deg	0.907	3	18657
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.724	5	1100
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.96	26.179	335
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.456	15	1423
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.804	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.114	0.2	1344
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	9642
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1788
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.241	1.404	4316
X-RAY DIFFRACTION	r_mcbond_other	1.241	1.404	4315
X-RAY DIFFRACTION	r_mcangle_it	1.788	2.095	5390
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.122	1.708	4276
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.748→1.793 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.395	400	-
R_work	0.327	7254	-
obs	-	-	97.1 %

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	0.9929	-0.1996	-0.0301	1.4918	0.0204	0.7791	-0.0483	-0.0269	-0.064	0.2357	0.0091	0.2106	-0.0132	-0.033	0.0392	0.1347	-0.0032	0.0691	0.072	0.0078	0.1054	-18.1375	-4.8867	41.5021
2	1.297	0.0899	-0.8251	3.22	0.2321	1.2756	-0.012	-0.1609	-0.1679	0.3307	-0.0539	0.1975	0.0671	0.0599	0.0659	0.0671	-0.0339	0.0692	0.0824	0.0142	0.1595	-24.332	-22.0009	41.4476
3	6.1464	0.9916	-1.5791	4.4479	-0.0824	2.2092	-0.2341	0.0051	-0.3169	-0.2603	0.0427	-0.0646	0.166	0.075	0.1914	0.0769	-0.0228	0.048	0.0595	-0.056	0.1865	-19.5752	-28.2144	28.9042
4	1.1251	-0.0662	-0.4717	1.5296	-0.156	0.6772	-0.0785	0.1352	-0.1849	-0.061	0.0113	0.0347	0.1182	0.016	0.0672	0.0642	-0.0085	0.0333	0.0785	-0.0265	0.0949	-11.5644	-15.5342	26.53
5	1.004	0.1128	-0.1691	1.2328	0.197	1.0227	0.008	-0.1127	-0.0669	0.1812	-0.0345	0.0835	0.0517	-0.0049	0.0266	0.1142	-0.0107	-0.002	0.0846	0.0025	0.0829	-24.8668	-5.7421	0.4538
6	1.2445	-0.4175	-0.4785	3.4462	0.0384	1.5411	-0.0518	-0.2291	-0.1753	0.4212	-0.0363	0.1257	0.1428	0.1699	0.0881	0.1161	-0.0062	0.0123	0.0807	0.0177	0.1086	-27.4841	-24.0786	-0.6342
7	8.1545	-1.6944	-1.4846	5.4007	0.1043	3.3008	0.2365	-0.0329	-0.1047	-0.0674	-0.1995	-0.2328	0.4508	0.4045	-0.0369	0.1476	0.0287	-0.046	0.0869	0.0011	0.0857	-23.6229	-26.3387	-7.6242
8	1.0925	0.4881	0.1216	1.5057	0.0294	0.2106	0.0251	0.0965	-0.1342	-0.1134	-0.0551	-0.101	0.1336	0.0534	0.03	0.1206	0.0172	0.0103	0.079	-0.0196	0.0808	-18.4273	-18.0308	-14.9715
9	0.663	0.1989	-0.0879	0.826	-0.1258	0.6536	0.0327	-0.0927	0.0181	0.1067	-0.0503	-0.02	-0.0322	0.0472	0.0176	0.0849	-0.007	-0.0168	0.0931	-0.0038	0.0642	-16.6659	5.5109	-0.03
10	2.1478	-0.0237	0.1398	2.1986	-0.0288	3.0941	0.0243	-0.2432	-0.042	0.1826	-0.0481	-0.0635	-0.2459	0.0914	0.0238	0.0822	-0.059	-0.0313	0.1135	0.0189	0.0669	-7.6911	16.8638	0.6555
11	1.8832	0.1907	1.2511	1.5052	0.0593	2.1846	-0.0553	-0.0743	0.1805	-0.1621	-0.0412	0.0116	-0.1862	-0.0463	0.0965	0.0764	-0.0224	-0.0201	0.0532	0.0114	0.0796	-15.9907	28.5743	-10.8112
12	1.3771	0.297	0.2808	1.4596	-0.2309	0.8644	-0.0199	0.0529	0.0575	-0.1447	-0.0009	0.0678	-0.0816	-0.0087	0.0208	0.1072	-0.0036	-0.0244	0.0778	-0.0001	0.0536	-22.1383	13.6593	-16.4299
13	0.7068	0.4576	-0.1654	1.6183	-0.1907	0.6174	-0.0074	-0.0472	0.0378	0.264	-0.0264	0.0497	-0.0668	0.0373	0.0338	0.1428	-0.0015	0.0233	0.0647	0.0045	0.0531	-11.8098	4.6309	42.7831
14	1.3256	-0.2523	0.4649	3.3947	-0.1128	1.2969	0.0083	-0.1317	0.0643	0.4011	-0.0488	0.049	-0.0216	-0.0956	0.0406	0.1509	-0.044	0.0222	0.1163	-0	0.0677	-6.9055	19.8244	42.4444
15	3.4374	-0.0198	0.4469	2.6296	0.2228	1.669	-0.0017	0.0355	0.1928	0.0604	-0.0422	0.0976	-0.0754	-0.0681	0.0439	0.1132	-0.0128	0.0432	0.1055	0.0129	0.0799	-9.1335	27.6474	32.6039
16	0.9213	0.2915	0.1564	2.019	-0.0408	0.3773	-0.0297	0.0069	0.0432	-0.1024	0.0193	0.1979	-0.0511	-0.0661	0.0104	0.1105	-0.0288	0.0005	0.0923	0.0098	0.0562	-15.9262	14.8869	26.1869

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 74
2	X-RAY DIFFRACTION	2	A	75 - 167
3	X-RAY DIFFRACTION	3	A	168 - 199
4	X-RAY DIFFRACTION	4	A	200 - 276
5	X-RAY DIFFRACTION	5	B	1 - 96
6	X-RAY DIFFRACTION	6	B	97 - 167
7	X-RAY DIFFRACTION	7	B	168 - 183
8	X-RAY DIFFRACTION	8	B	184 - 276
9	X-RAY DIFFRACTION	9	C	2 - 86
10	X-RAY DIFFRACTION	10	C	87 - 137
11	X-RAY DIFFRACTION	11	C	138 - 203
12	X-RAY DIFFRACTION	12	C	204 - 276
13	X-RAY DIFFRACTION	13	D	1 - 88
14	X-RAY DIFFRACTION	14	D	89 - 156
15	X-RAY DIFFRACTION	15	D	157 - 194
16	X-RAY DIFFRACTION	16	D	195 - 276

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