PDB-6slh: Conformational flexibility within the small domain of human serin...

ID or keywords:

Entry

Database: PDB / ID: 6slh

Title

Conformational flexibility within the small domain of human serine racemase.

Components

Serine racemase

Keywords

ISOMERASE / PLP-dependent /

D-serine /

racemization /

NMDA receptor

Function / homology

Function and homology information

D-serine biosynthetic process /

serine racemase /

threonine racemase activity / serine family amino acid metabolic process /

serine racemase activity /

D-serine ammonia-lyase /

D-serine ammonia-lyase activity /

L-serine ammonia-lyase /

L-serine ammonia-lyase activity / D-serine metabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89 Å

Authors

Koulouris, C.R. / Bax, B. / Atack, J. / Roe, S.M.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Conformational flexibility within the small domain of human serine racemase.
Authors: Koulouris, C.R. / Bax, B.D. / Atack, J.R. / Roe, S.M.

History

Deposition	Aug 19, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 12, 2020	Provider: repository / Type: Initial release
Revision 1.1	Feb 19, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6slh.cif.gz	463.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6slh.ent.gz		Display	PDB format
PDBx/mmJSON format	6slh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sl/6slh ftp://data.pdbj.org/pub/pdb/validation_reports/sl/6slh	HTTPS FTP

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Related structure data

Related structure data	3hmkS S: Starting model for refinement
Similar structure data	4887 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

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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 (3)

Deposited unit

AAA: Serine racemase

BBB: Serine racemase

CCC: Serine racemase

DDD: Serine racemase

hetero molecules

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

1

AAA: Serine racemase

CCC: Serine racemase

hetero molecules

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

2

BBB: Serine racemase

DDD: Serine racemase

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.200, 155.740, 85.580
Angle α, β, γ (deg.)	90.000, 98.480, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Serine racemase / / D-serine ammonia-lyase / D-serine dehydratase / L-serine ammonia-lyase / L-serine dehydratase Mass: 37683.977 Da / Num. of mol.: 4 / Mutation: C2D, C6D Source method: isolated from a genetically manipulated source Details: PLP cofactor is covalently bound to Lys56 / Source: (gene. exp.) Homo sapiens (human) / Gene: SRR / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus References: UniProt: Q9GZT4, serine racemase, D-serine ammonia-lyase, L-serine ammonia-lyase
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.1 Å³/Da / Density % sol: 41.44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM Bis-Tris pH 6.5, 15% PEG 3350, 250 mM MgCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.89→40.87 Å / Num. obs: 98693 / % possible obs: 99.2 % / Redundancy: 3.4 % / R_rim(I) all: 0.071 / Net I/av σ(I): 10.5 / Net I/σ(I): 10.5
Reflection shell	Resolution: 1.89→1.92 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4996 / R_rim(I) all: 1.086

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
xia2		data reduction
xia2		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3HMK

3hmk

Resolution: 1.89→40.87 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.953 / SU B: 6.837 / SU ML: 0.115 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.141
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2158	4925	4.992 %
R_work	0.1723	-	-
all	0.174	-	-
obs	-	98652	99.168 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 53.157 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.246 Å²	0 Å²	0.869 Å²
2-	-	1.593 Å²	0 Å²
3-	-	-	-0.581 Å²

Refinement step

Cycle: LAST / Resolution: 1.89→40.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9302	0	28	532	9862

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	10447
X-RAY DIFFRACTION	r_angle_refined_deg	1.859	1.626	14350
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.974	5	1431
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.977	24.094	381
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.436	15	1575
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.781	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.127	0.2	1481
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	7888
X-RAY DIFFRACTION	r_nbd_refined	0.24	0.2	5267
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	6986
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.176	0.2	638
X-RAY DIFFRACTION	r_metal_ion_refined	0.244	0.2	14
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.285	0.2	64
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.179	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	2.662	3.1	5621
X-RAY DIFFRACTION	r_mcangle_it	4.165	4.608	7087
X-RAY DIFFRACTION	r_scbond_it	3.059	3.257	4826
X-RAY DIFFRACTION	r_scangle_it	4.561	4.826	7263
X-RAY DIFFRACTION	r_lrange_it	14.358	57.637	48864

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 (%)
1.89-1.939	0.302	351	0.294	6987	X-RAY DIFFRACTION	99.7011
1.939-1.992	0.291	354	0.263	6793	X-RAY DIFFRACTION	99.707
1.992-2.05	0.244	360	0.232	6522	X-RAY DIFFRACTION	99.8404
2.05-2.113	0.242	343	0.211	6385	X-RAY DIFFRACTION	99.7775
2.113-2.182	0.246	322	0.201	6246	X-RAY DIFFRACTION	99.9239
2.182-2.258	0.208	292	0.183	6014	X-RAY DIFFRACTION	99.8259
2.258-2.343	0.226	328	0.171	5752	X-RAY DIFFRACTION	99.885
2.343-2.438	0.221	294	0.173	5597	X-RAY DIFFRACTION	99.7291
2.438-2.546	0.232	298	0.171	5358	X-RAY DIFFRACTION	99.5424
2.546-2.67	0.225	267	0.172	5075	X-RAY DIFFRACTION	99.4045
2.67-2.814	0.223	264	0.167	4813	X-RAY DIFFRACTION	99.1408
2.814-2.984	0.219	222	0.176	4586	X-RAY DIFFRACTION	99.0727
2.984-3.189	0.24	214	0.168	4293	X-RAY DIFFRACTION	98.5999
3.189-3.443	0.201	209	0.152	3987	X-RAY DIFFRACTION	98.267
3.443-3.769	0.182	192	0.155	3637	X-RAY DIFFRACTION	97.9785
3.769-4.21	0.184	178	0.143	3271	X-RAY DIFFRACTION	97.4019
4.21-4.853	0.212	156	0.142	2919	X-RAY DIFFRACTION	97.2486
4.853-5.925	0.23	127	0.182	2455	X-RAY DIFFRACTION	97.2139
5.925-8.3	0.219	94	0.194	1917	X-RAY DIFFRACTION	96.7292
8.3-40.8	0.186	60	0.182	1120	X-RAY DIFFRACTION	97.763

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	2.6173	-0.4237	-0.065	1.1919	-0.1355	0.0622	0.2564	0.5372	0.3535	-0.2431	-0.1849	-0.1352	0.0855	-0.0684	-0.0715	0.2713	0.072	0.0083	0.3898	0.1368	0.3651	-9.6684	-16.6556	28.4434
2	0.7691	-0.0059	0.1271	0.3124	0.0488	0.5563	0.0593	-0.0255	-0.035	0.0052	-0.006	-0.0543	0.0229	-0.0118	-0.0533	0.2662	0.0114	-0.0166	0.2003	0.0141	0.3037	9.7672	-26.0503	42.4415
3	1.3584	1.9255	0.8812	2.8333	1.1343	1.6135	0.3208	0.0088	0.0227	0.7827	-0.096	0.1348	-0.1354	-0.2124	-0.2248	0.9198	-0.2483	0.2481	0.2356	0.0433	0.2334	-17.3454	-69.8444	88.6028
4	0.973	0.2493	-0.2256	1.1688	0.5038	1.5605	-0.052	0.0077	0.0308	0.1293	0.1324	-0.2193	0.4278	-0.0878	-0.0805	0.4196	-0.0166	-0.0772	0.102	0.022	0.2625	4.7078	-60.654	79.5156
5	4.815	-2.9098	0.3485	1.7827	-0.3639	1.0468	0.0265	-0.1108	-0.7087	-0.151	0.0282	0.4348	0.6923	-0.0337	-0.0546	0.6053	0.0911	-0.0294	0.0955	-0.0661	0.4827	17.0968	-67.7228	35.0298
6	0.3153	0.7515	0.1108	2.7101	-0.7321	1.13	0.1007	0.0403	0.1532	0.1171	0.0507	0.5308	0.1317	0.0637	-0.1514	0.3078	-0.0307	-0.0484	0.0583	-0.0076	0.4387	-5.7927	-58.0359	42.1543
7	1.2632	0.6664	0.5201	1.1424	-0.4424	0.921	0.3622	-0.1031	0.1376	0.4187	-0.2076	0.1652	-0.0055	0.0532	-0.1545	0.3113	-0.1067	0.046	0.2978	-0.0251	0.3038	9.1842	-19.1947	89.8695
8	0.8823	-0.0357	-0.0483	0.3582	-0.18	0.9057	0.0857	-0.0408	-0.052	-0.0351	-0.0387	0.0488	0.0205	-0.0555	-0.0471	0.2468	-0.0129	-0.0113	0.2551	-0.0027	0.2636	-11.0096	-28.9986	76.0437

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A*	77 - 150
2	X-RAY DIFFRACTION	2	ALL	A*	7 - 55
3	X-RAY DIFFRACTION	2	ALL	A*	157 - 295
4	X-RAY DIFFRACTION	2	ALL	A*	307 - 315
5	X-RAY DIFFRACTION	3	ALL	B*	77 - 150
6	X-RAY DIFFRACTION	4	ALL	B*	7 - 55
7	X-RAY DIFFRACTION	4	ALL	B*	157 - 295
8	X-RAY DIFFRACTION	4	ALL	B*	307 - 315
9	X-RAY DIFFRACTION	5	ALL	C*	77 - 150
10	X-RAY DIFFRACTION	6	ALL	C*	7 - 55
11	X-RAY DIFFRACTION	6	ALL	C*	157 - 295
12	X-RAY DIFFRACTION	6	ALL	C*	307 - 315
13	X-RAY DIFFRACTION	7	ALL	D*	77 - 150
14	X-RAY DIFFRACTION	8	ALL	D*	7 - 55
15	X-RAY DIFFRACTION	8	ALL	D*	157 - 295
16	X-RAY DIFFRACTION	8	ALL	D*	307 - 315

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