PDB-7nbc: Crystal structure of human serine racemase in complex with DSiP f...

ID or keywords:

Entry

Database: PDB / ID: 7nbc

Title

Crystal structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen.

Components

Serine racemase

Keywords

ISOMERASE / Racemase / XChem / Inhibitor

Function / homology

Function and homology information

: / D-serine biosynthetic process / serine racemase / threonine racemase activity / serine racemase activity / D-serine ammonia-lyase / L-serine ammonia-lyase / D-serine ammonia-lyase activity / 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: 1.71 Å

Authors

Koulouris, C.R. / Roe, S.M.

Funding support

United Kingdom, 1items

Citation

Journal: Commun Biol / Year: 2022
Title: Tyrosine 121 moves revealing a ligandable pocket that couples catalysis to ATP-binding in serine racemase.
Authors: Koulouris, C.R. / Gardiner, S.E. / Harris, T.K. / Elvers, K.T. / Mark Roe, S. / Gillespie, J.A. / Ward, S.E. / Grubisha, O. / Nicholls, R.A. / Atack, J.R. / Bax, B.D.

History

Deposition	Jan 26, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 3, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 27, 2022	Group: Database references / Category: citation / citation_author / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	May 4, 2022	Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3	Jan 31, 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 / citation / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_id_ISSN

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7nbc.cif.gz	448.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7nbc.ent.gz		Display	PDB format
PDBx/mmJSON format	7nbc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7nbc_validation.pdf.gz	785.1 KB	Display	wwPDB validaton report
Full document	7nbc_full_validation.pdf.gz	806.8 KB	Display
Data in XML	7nbc_validation.xml.gz	58.2 KB	Display
Data in CIF	7nbc_validation.cif.gz	84 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nb/7nbc ftp://data.pdbj.org/pub/pdb/validation_reports/nb/7nbc	HTTPS FTP

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Related structure data

Related structure data	6zspC 6zujSC 7nbdC 7nbfC 7nbgC 7nbhC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	7nbg-1 7nbd-1 6zuj-1 7nbf-1 2brv-d 1n7n-d 3b8v-1 5jy8-d 3b8w-1 6r7u-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 - 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

153 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
Evidence: gel filtration
76.8 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
76.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.150, 154.860, 85.480
Angle α, β, γ (deg.)	90.000, 98.080, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein	Serine racemase / D-serine ammonia-lyase / D-serine dehydratase / L-serine ammonia-lyase / L-serine dehydratase Mass: 37455.863 Da / Num. of mol.: 4 / Mutation: C2D, C6D Source method: isolated from a genetically manipulated source Details: Cofactor pyridoxal-5'-phosphate (PLP, LLP) is covalently bound to lysine 56 Source: (gene. exp.) Homo sapiens (human) / Gene: SRR / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus (DE3)-RIL References: UniProt: Q9GZT4, serine racemase, D-serine ammonia-lyase, L-serine ammonia-lyase

#1: Protein

Serine racemase / D-serine ammonia-lyase / D-serine dehydratase / L-serine ammonia-lyase / L-serine dehydratase

Mass: 37455.863 Da / Num. of mol.: 4 / Mutation: C2D, C6D
Source method: isolated from a genetically manipulated source
Details: Cofactor pyridoxal-5'-phosphate (PLP, LLP) is covalently bound to lysine 56
Source: (gene. exp.)

Homo sapiens (human) / Gene: SRR / Plasmid: pET-15b / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus (DE3)-RIL
References: UniProt: Q9GZT4, serine racemase, D-serine ammonia-lyase, L-serine ammonia-lyase

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Non-polymers , 9 types, 905 molecules

#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / D-serine ammonia-lyase / D-serine dehydratase / L-serine ammonia-lyase / L-serine dehydratase / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 4 / Mutation: C2D, C6D Source method: isolated from a genetically manipulated source Formula: C₈H₁₀NO₆P Details: Cofactor pyridoxal-5'-phosphate (PLP, LLP) is covalently bound to lysine 56 References: serine racemase, D-serine ammonia-lyase, L-serine ammonia-lyase
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#8: Chemical	ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₁₂O₃ / Comment: precipitant*YM
#9: Chemical	ChemComp-BP4 / biphenyl-4-ylacetic acid Mass: 212.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₁₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 867 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.11 Å³/Da / Density % sol: 41.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 100 mM MES pH 6.2 100 mM calcium chloride 5% ethylene glycol 20% PEG Smear Broad

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91587 Å / Relative weight: 1
Reflection	Resolution: 1.71→77.6 Å / Num. obs: 130785 / % possible obs: 98.2 % / Redundancy: 3.4 % / CC_1/2: 0.997 / R_merge(I) obs: 0.067 / R_pim(I) all: 0.093 / Net I/σ(I): 8.3
Reflection shell	Resolution: 1.71→1.74 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.948 / Mean I/σ(I) obs: 1 / Num. unique obs: 6420 / CC_1/2: 0.305 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
DIALS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6ZUJ

6zuj

Resolution: 1.71→77.4 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.958 / SU B: 4.663 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.106 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2015	6527	4.992 %
R_work	0.1744	124213	-
all	0.176	-	-
obs	-	130740	98.094 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.375 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.361 Å²	0 Å²	0.225 Å²
2-	-	0.417 Å²	0 Å²
3-	-	-	-0.115 Å²

Refinement step

Cycle: LAST / Resolution: 1.71→77.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9507	0	136	867	10510

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	10532
X-RAY DIFFRACTION	r_angle_refined_deg	1.356	1.627	14460
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.459	5	1425
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.742	24.338	408
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.537	15	1673
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.903	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	1459
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	7958
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	5515
X-RAY DIFFRACTION	r_nbtor_refined	0.311	0.2	7068
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	812
X-RAY DIFFRACTION	r_metal_ion_refined	0.165	0.2	33
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.223	0.2	107
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.239	0.2	33
X-RAY DIFFRACTION	r_mcbond_it	1.483	2.55	5507
X-RAY DIFFRACTION	r_mcangle_it	2.493	3.799	6997
X-RAY DIFFRACTION	r_scbond_it	1.924	2.759	5025
X-RAY DIFFRACTION	r_scangle_it	3.003	4.068	7463
X-RAY DIFFRACTION	r_lrange_it	9.728	49.667	52847

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 (%)
1.71-1.754	0.325	453	0.32	9070	X-RAY DIFFRACTION	97.233
1.754-1.802	0.298	456	0.307	8913	X-RAY DIFFRACTION	97.5531
1.802-1.855	0.282	480	0.267	8629	X-RAY DIFFRACTION	97.5372
1.855-1.912	0.27	424	0.238	8417	X-RAY DIFFRACTION	97.9829
1.912-1.974	0.224	431	0.212	8159	X-RAY DIFFRACTION	97.9811
1.974-2.044	0.225	420	0.2	7927	X-RAY DIFFRACTION	98.0846
2.044-2.121	0.211	412	0.185	7643	X-RAY DIFFRACTION	98.2557
2.121-2.207	0.203	362	0.171	7401	X-RAY DIFFRACTION	98.4028
2.207-2.305	0.192	395	0.16	7096	X-RAY DIFFRACTION	98.4621
2.305-2.418	0.199	367	0.159	6738	X-RAY DIFFRACTION	98.3391
2.418-2.548	0.191	344	0.161	6444	X-RAY DIFFRACTION	98.7776
2.548-2.703	0.208	312	0.165	6121	X-RAY DIFFRACTION	98.954
2.703-2.889	0.191	299	0.156	5736	X-RAY DIFFRACTION	98.8048
2.889-3.12	0.202	290	0.159	5357	X-RAY DIFFRACTION	98.8102
3.12-3.418	0.203	272	0.158	4927	X-RAY DIFFRACTION	98.6153
3.418-3.82	0.171	251	0.15	4405	X-RAY DIFFRACTION	98.3939
3.82-4.41	0.149	191	0.136	3953	X-RAY DIFFRACTION	97.9437
4.41-5.397	0.168	170	0.15	3299	X-RAY DIFFRACTION	97.6908
5.397-7.618	0.226	139	0.201	2538	X-RAY DIFFRACTION	97.3101
7.618-77.4	0.201	59	0.188	1440	X-RAY DIFFRACTION	96.6473

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	1.1568	-0.242	-0.0047	0.9898	0.352	2.0053	0.0909	0.0898	0.1004	-0.2713	-0.0088	-0.0377	-0.0765	0.0329	-0.0821	0.0802	0.0181	0.023	0.0547	0.021	0.0572	-9.0966	-16.3008	28.4017
2	0.4083	0.0853	-0.0021	0.4119	0.068	0.2681	0.0206	-0.0169	-0.0315	0.0126	0.0043	-0.0695	0.0041	-0.0071	-0.0248	0.0356	0.0042	0.0073	0.0219	0.0143	0.069	10.428	-25.921	42.1801
3	3.9102	1.9625	-0.4733	1.3228	-0.2085	0.0911	0.4011	-0.4661	-0.1714	0.6032	-0.3729	-0.1118	-0.0417	-0.0199	-0.0282	0.5293	-0.145	-0.0192	0.24	0.1039	0.0494	-16.2452	-69.823	87.8217
4	0.4142	-0.0874	-0.1002	0.8518	0.0779	0.486	0.0004	0.0035	0.0481	0.0321	0.0086	-0.1402	0.0575	-0.0231	-0.0089	0.0697	0.0085	-0.0035	0.0248	0.0049	0.0281	5.9827	-60.6386	79.3373
5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.0677	0	0	0.0677	0	0.0677	0	0	0
6	0.5307	0.1512	-0.0797	0.5891	-0.1402	0.2372	-0.0201	0.029	0.0822	0.0295	0.026	0.0928	0.0313	-0.0012	-0.0059	0.0708	-0.01	0.0056	0.0072	0.0041	0.045	-5.2779	-57.8641	41.6952
7	2.2704	1.1143	0.0413	1.5458	0.3011	1.7539	0.378	-0.1151	0.1695	0.4616	-0.2602	0.1206	0.0711	0.0517	-0.1179	0.1401	-0.08	0.0422	0.0715	-0.0369	0.0329	10.2379	-19.2623	89.6697
8	0.5788	-0.105	-0.0907	0.4163	-0.1278	0.541	0.0171	-0.009	-0.0232	0.0027	-0.0107	0.0551	0.0095	-0.0101	-0.0064	0.0318	-0.0046	0.0164	0.051	-0.0164	0.0321	-10.1297	-29.0483	75.8806

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	77 - 150
2	X-RAY DIFFRACTION	2	ALL	AAA	7 - 55
3	X-RAY DIFFRACTION	2	ALL	AAA	157 - 295
4	X-RAY DIFFRACTION	2	ALL	AAA	307 - 315
5	X-RAY DIFFRACTION	3	ALL	BBB	77 - 150
6	X-RAY DIFFRACTION	4	ALL	BBB	7 - 55
7	X-RAY DIFFRACTION	4	ALL	BBB	157 - 295
8	X-RAY DIFFRACTION	4	ALL	BBB	307 - 315
9	X-RAY DIFFRACTION	5	ALL	BBB	77 - 150
10	X-RAY DIFFRACTION	6	ALL	CCC	7 - 55
11	X-RAY DIFFRACTION	6	ALL	CCC	157 - 295
12	X-RAY DIFFRACTION	6	ALL	CCC	307 - 315
13	X-RAY DIFFRACTION	7	ALL	DDD	77 - 150
14	X-RAY DIFFRACTION	8	ALL	DDD	7 - 55
15	X-RAY DIFFRACTION	8	ALL	DDD	157 - 295
16	X-RAY DIFFRACTION	8	ALL	DDD	307 - 315

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