PDB-4n0w: X-ray crystal structure of a serine hydroxymethyltransferase from...

ID or keywords:

Entry

Database: PDB / ID: 4n0w

Title

X-ray crystal structure of a serine hydroxymethyltransferase from Burkholderia cenocepacia with covalently attached pyridoxal phosphate

Components

Serine hydroxymethyltransferase

Keywords

TRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / serine hydroxymethyltransferase

Function / homology

Function and homology information

glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / L-serine catabolic process / tetrahydrofolate interconversion / cobalt ion binding / folic acid metabolic process / pyridoxal phosphate binding / zinc ion binding / cytosol
Similarity search - Function

Biological species

Burkholderia cenocepacia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.65 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: X-ray crystal structure of a serine hydroxymethyltransferase from Burkholderia cenocepacia with covalently attached pyridoxal phosphate
Authors: Fairman, J.W. / Jensen, M.M. / Sullivan, A.H. / Abendroth, J. / Edwards, T.E. / Lorimer, D.

History

Deposition	Oct 2, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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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Download

PDBx/mmCIF format	4n0w.cif.gz	659.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4n0w.ent.gz	544.9 KB	Display	PDB format
PDBx/mmJSON format	4n0w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4n0w_validation.pdf.gz	478.3 KB	Display	wwPDB validaton report
Full document	4n0w_full_validation.pdf.gz	488.1 KB	Display
Data in XML	4n0w_validation.xml.gz	72.2 KB	Display
Data in CIF	4n0w_validation.cif.gz	107.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n0/4n0w ftp://data.pdbj.org/pub/pdb/validation_reports/n0/4n0w	HTTPS FTP

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Related structure data

Related structure data	4msoS S: Starting model for refinement
Similar structure data	2d5y-1 4ot8-1 4otl-2 2vgw-1 5u24-2 1ase-1 2vgt-1 2vmx-1 1cq7-1 4uqv-6 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
Other databases	TargetTrack: SSGCID-BuceA.00008.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Serine hydroxymethyltransferase

B: Serine hydroxymethyltransferase

C: Serine hydroxymethyltransferase

D: Serine hydroxymethyltransferase

hetero molecules

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

1

A: Serine hydroxymethyltransferase

C: Serine hydroxymethyltransferase

hetero molecules

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

2

B: Serine hydroxymethyltransferase

D: Serine hydroxymethyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.580, 178.650, 75.660
Angle α, β, γ (deg.)	90.000, 114.700, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	VAL	VAL	A	A	1 - 413	10 - 422
2	1	MET	MET	VAL	VAL	B	B	1 - 413	10 - 422
1	2	MET	MET	TYR	TYR	A	A	1 - 414	10 - 423
2	2	MET	MET	TYR	TYR	C	C	1 - 414	10 - 423
1	3	PHE	PHE	TYR	TYR	A	A	2 - 414	11 - 423
2	3	PHE	PHE	TYR	TYR	D	D	2 - 414	11 - 423
1	4	MET	MET	VAL	VAL	B	B	1 - 413	10 - 422
2	4	MET	MET	VAL	VAL	C	C	1 - 413	10 - 422
1	5	PHE	PHE	VAL	VAL	B	B	2 - 413	11 - 422
2	5	PHE	PHE	VAL	VAL	D	D	2 - 413	11 - 422
1	6	PHE	PHE	TYR	TYR	C	C	2 - 414	11 - 423
2	6	PHE	PHE	TYR	TYR	D	D	2 - 414	11 - 423

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Serine hydroxymethyltransferase / SHMT / Serine methylase Mass: 46070.289 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: glyA, glyA1, BceJ2315_31420, BCAL3197 / Production host: Escherichia coli (E. coli) References: UniProt: B4ECY9, glycine hydroxymethyltransferase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1494 / 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: 2.19 Å³/Da / Density % sol: 43.71 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MCSG1 F11: 0.2 M ammonium sulfate, 0.1 M HEPES pH 7.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

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

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.65→50 Å / Num. all: 189363 / Num. obs: 188538 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 26.052 Å² / R_merge(I) obs: 0.056 / Net I/σ(I): 14.81

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
1.65-1.69		0.547	2.25	48531	13619	97.4
1.69-1.74		0.45	2.94	51619	13591	99.8
1.74-1.79		0.356	3.73	50368	13246	99.8
1.79-1.84		0.28	4.66	48987	12855	99.8
1.84-1.91		0.214	6.11	47524	12440	99.8
1.91-1.97		0.172	7.62	45988	12031	99.8
1.97-2.05		0.13	9.82	44626	11680	99.8
2.05-2.13		0.107	11.77	42872	11195	99.8
2.13-2.22		0.083	14.73	40855	10695	99.8
2.22-2.33		0.073	16.74	39185	10292	99.7
2.33-2.46		0.064	18.71	37173	9750	99.8
2.46-2.61		0.058	20.46	35131	9240	99.8
2.61-2.79		0.049	23.98	32858	8668	99.7
2.79-3.01		0.044	26.71	30389	8093	99.7
3.01-3.3		0.039	29.68	27681	7441	99.5
3.3-3.69		0.033	33.35	24786	6714	99.6
3.69-4.26		0.03	36.31	22028	5954	99.7
4.26-5.22		0.027	37.19	18622	5005	99.4
5.22-7.38		0.026	36.81	14664	3912	99.4
	7.38	0.023	38.67	7703	2117	97.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
REFMAC	5.7.0032	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MSO

4mso

Resolution: 1.65→45.05 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.965 / Occupancy max: 1 / Occupancy min: 0.27 / SU B: 3.293 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1751	9470	5 %	RANDOM
R_work	0.1561	-	-	-
obs	0.157	188538	99.72 %	-
all	-	189363	-	-

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 max: 63.98 Å² / B_iso mean: 23.81 Å² / B_iso min: 4.19 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.72 Å²	-0 Å²	0.27 Å²
2-	-	0.35 Å²	0 Å²
3-	-	-	-0.85 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→45.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12406	0	80	1494	13980

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	13011
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	12393
X-RAY DIFFRACTION	r_angle_refined_deg	1.43	1.963	17728
X-RAY DIFFRACTION	r_angle_other_deg	1.092	3	28460
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.639	5	1727
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.35	24.306	569
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.635	15	2073
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.934	15	79
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	1982
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	15140
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	2939
X-RAY DIFFRACTION	r_mcbond_it	0.466	0.872	6707
X-RAY DIFFRACTION	r_mcbond_other	0.466	0.872	6706
X-RAY DIFFRACTION	r_mcangle_it	0.734	1.306	8396

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	24746	0.07
1	2	B	24746	0.07
2	1	A	25143	0.07
2	2	C	25143	0.07
3	1	A	25193	0.06
3	2	D	25193	0.06
4	1	B	25050	0.06
4	2	C	25050	0.06
5	1	B	24574	0.07
5	2	D	24574	0.07
6	1	C	24969	0.07
6	2	D	24969	0.07

LS refinement shell

Resolution: 1.65→1.693 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.291	668	-
R_work	0.275	12937	-
all	-	13605	-
obs	-	-	97.46 %

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	5.5373	3.6292	-1.5977	7.4817	-5.6914	7.5636	0.1687	-0.0727	-0.1191	0.0451	0.1698	0.475	0.2138	-0.746	-0.3385	0.0913	0.0573	-0.0245	0.277	-0.015	0.1312	6.2962	66.3832	75.7968
2	0.9692	-0.2716	-0.2939	1.3397	-0.6711	1.464	-0.0283	-0.0362	-0.0335	0.053	-0.0003	0.0259	0.0399	-0.1189	0.0286	0.0174	-0.0099	-0.0034	0.0397	-0.0214	0.0276	22.89	52.8466	71.1529
3	2.0342	0.5427	-0.1653	0.7523	-0.1417	1.5664	0.0558	-0.0897	0.3065	-0.0338	-0.064	-0.1475	-0.0795	0.3496	0.0082	0.0298	-0.002	0.0162	0.0918	-0.0075	0.1385	43.1454	58.3841	72.8977
4	1.8623	-0.2288	2.2306	1.2942	-1.6564	5.1734	-0.0418	-0.046	0.1069	-0.0483	-0.1474	-0.3234	-0.1247	0.4251	0.1892	0.0414	0.001	0.0623	0.1755	-0.0169	0.1879	52.5835	60.0622	63.9651
5	1.7021	-0.1864	0.0069	0.743	-0.4329	1.5617	0.0311	0.0324	-0.0602	-0.0873	-0.0664	-0.1094	0.1938	0.1148	0.0352	0.0376	0.0201	-0.0024	0.012	0.0025	0.0352	36.509	50.6959	67.7227
6	1.4217	-0.3201	-0.3044	1.6228	-0.5294	1.2793	0.0894	0.107	0.1476	-0.1791	-0.0805	-0.1151	-0.0599	-0.0305	-0.0089	0.0836	0.0573	0.0273	0.0453	0.0198	0.0301	32.4276	71.8672	49.6934
7	1.388	0.3433	0.0898	2.645	0.5617	5	0.14	0.0668	0.2585	-0.1385	-0.069	0.0009	-0.1987	0.0913	-0.0711	0.117	-0.0502	0.0295	0.0499	0.0109	0.0812	9.57	32.9588	60.1273
8	1.151	-0.5221	-0.3436	2.6555	-0.0024	1.6418	0.005	0.1203	-0.1253	-0.2629	-0.0308	0.0316	0.338	0.0437	0.0258	0.1795	0.0171	-0.034	0.0467	-0.0297	0.0349	-1.278	10.4786	54.739
9	2.0902	1.5546	-1.2563	3.9059	-2.7855	2.0284	0.1024	0.0295	-0.3316	-0.4024	-0.3491	-0.2653	0.3387	0.3224	0.2468	0.5164	0.2233	0.0859	0.2512	-0.0386	0.1809	15.1906	-1.7807	43.0916
10	0.9713	-0.3623	-0.4435	2.5323	0.0199	1.7117	0.091	0.2427	-0.1494	-0.4973	-0.154	0.0657	0.2646	0.0136	0.0631	0.2305	0.0359	-0.0295	0.0848	-0.0486	0.0525	1.15	8.5897	47.7944
11	2.0407	0.4144	-0.1529	1.346	-0.4383	2.3352	0.2077	0.2265	0.0718	-0.3793	-0.2727	-0.3105	0.168	0.6869	0.065	0.2993	0.1049	0.1312	0.3524	0.0482	0.0996	22.7895	21.2875	40.6349
12	8.0261	1.4518	-2.099	1.9594	-0.698	1.0449	0.4008	-0.1275	0.6994	-0.0232	-0.3259	-0.5035	-0.189	0.5395	-0.075	0.3392	-0.0631	0.1371	0.5416	0.1129	0.3199	25.0109	36.1442	45.5701
13	1.6059	-0.2332	-1.3784	1.4218	2.2778	7.0308	-0.0597	0.1474	0.0248	-0.1337	0.0351	0.1553	-0.1941	-0.3577	0.0246	0.0584	-0.0396	-0.0056	0.0891	-0.0034	0.0947	13.1249	47.6547	75.2629
14	1.7537	0.1659	0.5325	0.7657	0.2051	2.0303	0.0238	-0.011	0.1241	0.0163	0.023	-0.0527	-0.1864	0.0601	-0.0469	0.0389	0.0161	-0.0098	0.0308	-0.0279	0.0355	26.7101	69.2578	80.3921
15	4.7628	-3.0691	-2.9467	2.7293	3.3982	11.0951	0.0191	-0.1921	-0.1348	-0.1088	0.0764	0.0031	-0.1056	0.5517	-0.0955	0.1197	0.0608	-0.0888	0.2146	-0.0722	0.1162	35.8144	55.0198	94.9728
16	1.0337	0.0488	0.2086	0.5453	-0.1461	1.7326	-0.0056	-0.2495	0.0596	0.1773	0.0173	-0.0835	-0.139	0.0881	-0.0117	0.0789	0.0127	-0.029	0.0913	-0.046	0.0597	29.5621	66.5265	95.5731
17	0.5338	0.3514	-0.3267	2.0125	-0.6187	1.6642	-0.0903	-0.1295	-0.0729	0.1824	0.0705	0.0222	0.1811	-0.1164	0.0199	0.1148	0.0217	0.0347	0.139	-0.0113	0.0346	14.4681	49.2226	101.2772
18	3.0768	0.3497	1.0019	6.4258	-4.0249	4.1595	-0.1117	-0.1261	-0.3058	-0.2731	0.288	0.2445	0.6168	-0.5941	-0.1763	0.2379	-0.1135	0.0578	0.2615	-0.0094	0.0749	5.7577	38.6497	94.5794
19	1.1334	-0.6587	-0.8431	1.2037	-1.8328	10.6739	0.2415	0.2634	0.133	-0.281	-0.266	0.0736	-0.2695	0.2657	0.0244	0.1622	0.035	-0.0562	0.1048	0.0131	0.1486	-12.0137	27.5941	58.7408
20	1.2727	-0.0415	-0.3708	1.7259	-0.4191	1.3047	-0.0058	-0.0624	-0.1348	-0.1599	-0.0468	-0.104	0.1881	0.1983	0.0527	0.0713	-0.0035	0.0135	0.0587	-0.0011	0.0309	7.872	15.1079	69.2693
21	3.6651	-1.2016	-1.5145	2.917	0.5471	0.8378	-0.0664	-0.1586	-0.4198	0.0721	-0.1286	-0.0656	0.2983	0.0804	0.195	0.35	0.0009	0.0131	0.0767	0.0681	0.1283	-1.2921	-0.7125	84.4618
22	1.5448	0.0506	-0.6822	0.802	-0.2762	1.1208	0.0289	-0.2255	-0.0715	0.1003	-0.0475	-0.0356	0.0193	0.1737	0.0186	0.0493	-0.0304	-0.0127	0.0657	0.0054	0.0335	-0.0462	16.1135	79.999
23	1.0276	0.6831	-0.1588	2.7591	-0.7901	1.054	0.0237	0.049	-0.0187	-0.0632	0.0376	0.3512	0.1433	-0.2317	-0.0613	0.0356	-0.0456	-0.0026	0.0786	-0.0007	0.1212	-24.0505	14.0499	77.8407
24	10.495	0.8223	-0.7998	4.8541	0.5541	2.4548	0.2672	0.1913	0.5598	0.0177	-0.0653	0.5184	-0.249	-0.3267	-0.2019	0.0685	0.0411	-0.0062	0.0749	0.027	0.1429	-23.7657	30.7133	73.4504

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 21
2	X-RAY DIFFRACTION	2	A	22 - 86
3	X-RAY DIFFRACTION	3	A	87 - 135
4	X-RAY DIFFRACTION	4	A	136 - 186
5	X-RAY DIFFRACTION	5	A	187 - 282
6	X-RAY DIFFRACTION	6	A	283 - 415
7	X-RAY DIFFRACTION	7	B	1 - 40
8	X-RAY DIFFRACTION	8	B	41 - 135
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