PDB-3gzd: Human selenocysteine lyase, P1 crystal form

ID or keywords:

Entry

Database: PDB / ID: 3gzd

Title

Human selenocysteine lyase, P1 crystal form

Components

(Selenocysteine lyase) x 2

Keywords

LYASE / STRUCTURAL GENOMICS / SCLY / selenocysteine / human / PYRIDOXAL-5'-PHOSPHATE / PLP / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

vitamin B6 binding / selenocysteine catabolic process / selenocysteine lyase / selenocysteine lyase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / amino acid metabolic process / amino acid binding / catalytic complex / transferase activity / Golgi apparatus ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Karlberg, T. / Hogbom, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...

Citation

Journal: Plos One / Year: 2012
Title: Biochemical discrimination between selenium and sulfur 1: a single residue provides selenium specificity to human selenocysteine lyase.
Authors: Collins, R. / Johansson, A.L. / Karlberg, T. / Markova, N. / van den Berg, S. / Olesen, K. / Hammarstrom, M. / Flores, A. / Schuler, H. / Schiavone, L.H. / Brzezinski, P. / Arner, E.S. / Hogbom, M.

History

Deposition	Apr 7, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 28, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jun 13, 2012	Group: Database references
Revision 1.3	Nov 1, 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_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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 22, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5	Nov 20, 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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PDBx/mmCIF format	3gzd.cif.gz	329.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3gzd.ent.gz	265.7 KB	Display	PDB format
PDBx/mmJSON format	3gzd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3gzd_validation.pdf.gz	496.2 KB	Display	wwPDB validaton report
Full document	3gzd_full_validation.pdf.gz	508.1 KB	Display
Data in XML	3gzd_validation.xml.gz	64.1 KB	Display
Data in CIF	3gzd_validation.cif.gz	92.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gz/3gzd ftp://data.pdbj.org/pub/pdb/validation_reports/gz/3gzd	HTTPS FTP

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Related structure data

Related structure data	3gzcSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3a9x-d 3gzc-d 6z5f-1 3zwb-1 3a9z-d 3hjw-d 3lwp-d 3lwv-d 4j3v-d 6ici-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

Deposited unit

A: Selenocysteine lyase

B: Selenocysteine lyase

C: Selenocysteine lyase

D: Selenocysteine lyase

hetero molecules

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

1

A: Selenocysteine lyase

B: Selenocysteine lyase

hetero molecules

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

2

C: Selenocysteine lyase

D: Selenocysteine lyase

hetero molecules

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

Unit cell

Length a, b, c (Å)	66.640, 72.200, 89.430
Angle α, β, γ (deg.)	83.91, 68.39, 86.96
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

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

#1: Protein	Selenocysteine lyase / hSCL Mass: 47820.246 Da / Num. of mol.: 3 / Fragment: UNP residues 8-445 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCL, SCLY / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q96I15, selenocysteine lyase
#2: Protein	Selenocysteine lyase / hSCL Mass: 47788.180 Da / Num. of mol.: 1 / Fragment: UNP residues 8-445 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCL, SCLY / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q96I15, selenocysteine lyase
#3: Chemical	ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE Mass: 233.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₂NO₅P
#4: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 898 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	(1) THERE IS NATURAL VARIANT AT THE POSITION 175. (2) AUTHOR STATES THAT CYS IN CHAIN C HAS NOT ...(1) THERE IS NATURAL VARIANT AT THE POSITION 175. (2) AUTHOR STATES THAT CYS IN CHAIN C HAS NOT BEEN MODIFIED INTO THE PERSULFIDE AS JUDGED BY DISTANCE AND ELECTRON DENSITY.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: 50mM HEPES, 200mM Ammonium Nitrate, 25% PEG 3350, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 14, 2006 / Details: mirrors
Radiation	Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. all: 134466 / Num. obs: 134466 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / R_merge(I) obs: 0.051 / R_sym value: 0.123 / Net I/σ(I): 16.2
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 2 % / R_merge(I) obs: 0.527 / Mean I/σ(I) obs: 2.2 / Num. unique all: 20018 / R_sym value: 0.743 / % possible all: 93.5

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Processing

Software

Name	Version	Classification
ProDC		data collection
MOLREP		phasing
REFMAC	5.5.0035	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GZC

3gzc

Resolution: 1.8→29.59 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.938 / SU B: 6.404 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21731	6724	5 %	RANDOM
R_work	0.18373	-	-	-
all	0.1854	127741	-	-
obs	0.1854	127741	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 12.632 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.24 Å²	0.05 Å²	0.59 Å²
2-	-	0.49 Å²	0.03 Å²
3-	-	-	-1.17 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12162	0	76	898	13136

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	12527
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8465
X-RAY DIFFRACTION	r_angle_refined_deg	1.455	1.97	17009
X-RAY DIFFRACTION	r_angle_other_deg	2.8	3	20666
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.601	5	1584
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.651	23.932	557
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.515	15	2090
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.987	15	98
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	1934
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	13964
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2414
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	0.703	1.5	7910
X-RAY DIFFRACTION	r_mcbond_other	0.185	1.5	3192
X-RAY DIFFRACTION	r_mcangle_it	1.211	2	12770
X-RAY DIFFRACTION	r_scbond_it	2.013	3	4617
X-RAY DIFFRACTION	r_scangle_it	3.062	4.5	4233
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5018 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	loose positional	0.37	5
B	loose positional	0.47	5
C	loose positional	0.38	5
D	loose positional	0.45	5
A	loose thermal	1.84	10
B	loose thermal	1.67	10
C	loose thermal	1.52	10
D	loose thermal	1.74	10

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.295	491	-
R_work	0.277	9331	-
obs	-	-	100 %

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	0.1771	0.1347	-0.051	0.4207	-0.1167	0.5277	-0.022	0.0133	0.021	0.057	0.0445	0.0363	-0.0003	-0.0998	-0.0225	0.0917	0.0055	0.0047	0.1205	-0.0051	0.0821	28.35	12.885	36.934
2	0.1443	0.0802	-0.0947	0.3309	-0.1031	0.308	-0.0241	0.0219	0.0131	0.0107	0.0499	0.0058	-0.0419	-0.0776	-0.0258	0.0918	0.0088	-0.0046	0.1095	-0.0044	0.092	31.688	20.284	26.975
3	0.9963	0.3517	0.0078	0.5228	-0.0154	0.9375	0.083	-0.1135	0.0193	0.0731	-0.0309	-0.1179	-0.1684	0.1599	-0.0522	0.1127	-0.0382	-0.0238	0.0657	-0.0401	0.1122	54.156	30.916	40.475
4	0.0813	0.0149	-0.0116	0.3836	0.1101	0.2901	-0.0269	-0.0021	-0.0248	0.0256	0.0321	-0.0311	0.0213	-0.0288	-0.0052	0.0976	-0.0049	0.0073	0.1065	0.0069	0.0821	36.574	-2.956	37.581
5	0.222	-0.0734	-0.0397	0.2409	0.0179	0.3259	-0.0171	-0.0153	-0.0444	0.0084	0.0201	-0.0187	0.0561	-0.044	-0.0031	0.1096	-0.0091	0.014	0.0909	0.0061	0.0957	35.926	-12.679	32.036
6	1.2312	-0.0181	0.1247	0.5456	0.0579	0.7048	0.05	-0.0976	-0.1538	0.0784	0.013	0.1448	0.1043	-0.1794	-0.0631	0.1116	-0.0541	0.043	0.1657	0.0799	0.114	12.299	-19.262	47.687
7	0.1742	-0.1536	-0.016	0.4593	-0.0514	0.4055	0.0025	0.0255	-0.0222	-0.0212	0.011	0.0537	0.0375	0.005	-0.0136	0.0818	0.008	-0.0013	0.1075	-0.0106	0.0895	-5.089	-7.699	-0.514
8	0.2397	-0.0735	-0.0438	0.3108	-0.0362	0.5039	-0.012	0.0076	-0.0489	0.0164	0.0158	0.0205	0.0906	0.0285	-0.0039	0.0959	0.011	0.0066	0.0949	-0.0071	0.1041	-1.676	-14.953	9.914
9	1.3993	-0.233	0.2641	0.6415	0.306	1.0094	0.0858	0.1058	-0.1396	0.0296	-0.0001	-0.0972	0.2746	0.2537	-0.0857	0.1203	0.1091	-0.0078	0.1408	-0.0639	0.1237	19.983	-26.3	-4.105
10	0.2861	-0.1172	-0.0802	0.263	0.1354	0.3424	-0.0247	0.0044	0.0529	0.0194	0.0306	-0.0175	-0.0135	0.081	-0.006	0.078	0.0019	-0.0063	0.1195	0.0079	0.0844	0.822	13.218	2.638
11	0.3426	-0.0464	-0.0792	0.067	-0.0589	0.1944	0.015	0.0188	0.0646	-0.0066	-0.0048	-0.0507	-0.0155	0.0861	-0.0102	0.0777	-0.016	-0.0108	0.1426	0.0127	0.1047	5.699	15.157	0.012
12	1.1996	-0.2167	0.3794	0.2082	0.0134	0.9308	0.0251	0.0779	0.0777	-0.0088	-0.0267	0.0283	-0.1107	-0.107	0.0017	0.0615	0.0353	-0.0142	0.0988	0.054	0.0806	-21.915	23.884	-10.467

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	31 - 143
2	X-RAY DIFFRACTION	2	A	144 - 317
3	X-RAY DIFFRACTION	3	A	318 - 443
4	X-RAY DIFFRACTION	4	B	31 - 155
5	X-RAY DIFFRACTION	5	B	156 - 317
6	X-RAY DIFFRACTION	6	B	318 - 443
7	X-RAY DIFFRACTION	7	C	31 - 143
8	X-RAY DIFFRACTION	8	C	144 - 313
9	X-RAY DIFFRACTION	9	C	314 - 443
10	X-RAY DIFFRACTION	10	D	31 - 211
11	X-RAY DIFFRACTION	11	D	212 - 324
12	X-RAY DIFFRACTION	12	D	325 - 443

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