PDB-6i35: Crystal structure of human glycine decarboxylase (P-protein) boun...

ID or keywords:

Entry

Database: PDB / ID: 6i35

Title

Crystal structure of human glycine decarboxylase (P-protein) bound with pyridoxyl-glycine-5'-monophosphate

Components

Glycine dehydrogenase (decarboxylating), mitochondrial

Keywords

OXIDOREDUCTASE / mitochondrial / glycine decarboxylase / glycine cleavage system P-protein

Function / homology

Function and homology information

response to methylamine / response to lipoic acid / pyridoxal binding / glycine dehydrogenase (aminomethyl-transferring) / glycine dehydrogenase (decarboxylating) activity / glycine catabolic process / Glycine degradation / glycine decarboxylation via glycine cleavage system / glycine cleavage complex / glycine binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Van Laer, B. / Kapp, U. / Leonard, G. / Mueller-Dieckmann, C.

Citation

Journal: To Be Published
Title: Structural insights in human glycine decarboxylase and comparison with the Neanderthal variant
Authors: Van Laer, B. / Kapp, U. / Signor, L. / Leonard, G. / Mueller-Dieckmann, C.

History

Deposition	Nov 5, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6i35.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb6i35.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	6i35.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6i35_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	6i35_full_validation.pdf.gz	1.9 MB	Display
Data in XML	6i35_validation.xml.gz	137.3 KB	Display
Data in CIF	6i35_validation.cif.gz	193.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i3/6i35 ftp://data.pdbj.org/pub/pdb/validation_reports/i3/6i35	HTTPS FTP

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Related structure data

Related structure data	6i33SC 6i34C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	22457 6i34-2 6i34-1 6r5v-d 3u4a-d 6r5u-d 3u48-d 6i33-d 4lhd-d 1h41-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	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #59 - Nov 2004 Photosystem II similarity (1)

Deposited unit

A: Glycine dehydrogenase (decarboxylating), mitochondrial

B: Glycine dehydrogenase (decarboxylating), mitochondrial

C: Glycine dehydrogenase (decarboxylating), mitochondrial

D: Glycine dehydrogenase (decarboxylating), mitochondrial

hetero molecules

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

1

A: Glycine dehydrogenase (decarboxylating), mitochondrial

B: Glycine dehydrogenase (decarboxylating), mitochondrial

hetero molecules

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

2

C: Glycine dehydrogenase (decarboxylating), mitochondrial

D: Glycine dehydrogenase (decarboxylating), mitochondrial

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.660, 123.440, 197.670
Angle α, β, γ (deg.)	90.00, 97.93, 90.00
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	ARG	ARG	PRO	PRO	A	A	51 - 1004	8 - 961
2	1	ARG	ARG	PRO	PRO	B	B	51 - 1004	8 - 961
1	2	ALA	ALA	MET	MET	A	A	49 - 1005	6 - 962
2	2	ALA	ALA	MET	MET	C	C	49 - 1005	6 - 962
1	3	ARG	ARG	PRO	PRO	A	A	51 - 1004	8 - 961
2	3	ARG	ARG	PRO	PRO	D	D	51 - 1004	8 - 961
1	4	ARG	ARG	PRO	PRO	B	B	51 - 1004	8 - 961
2	4	ARG	ARG	PRO	PRO	C	C	51 - 1004	8 - 961
1	5	ARG	ARG	PRO	PRO	B	B	51 - 1004	8 - 961
2	5	ARG	ARG	PRO	PRO	D	D	51 - 1004	8 - 961
1	6	ARG	ARG	PRO	PRO	C	C	51 - 1004	8 - 961
2	6	ARG	ARG	PRO	PRO	D	D	51 - 1004	8 - 961

NCS ensembles :

ID
1
2
3
4
5
6

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Glycine dehydrogenase (decarboxylating), mitochondrial / Glycine cleavage system P protein / Glycine decarboxylase / Glycine dehydrogenase (aminomethyl-transferring) Mass: 109512.203 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLDC, GCSP / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P23378, glycine dehydrogenase (aminomethyl-transferring)

#1: Protein

Glycine dehydrogenase (decarboxylating), mitochondrial / Glycine cleavage system P protein / Glycine decarboxylase / Glycine dehydrogenase (aminomethyl-transferring)

Mass: 109512.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: GLDC, GCSP / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P23378, glycine dehydrogenase (aminomethyl-transferring)

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Non-polymers , 6 types, 1042 molecules

#2: Chemical	ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE Mass: 306.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-BCT / BICARBONATE ION Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO₃ / Comment: pH buffer*YM
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1024 / 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: 2.38 Å³/Da / Density % sol: 48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7, 6 % PEG3350, 10 mM DTT

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 14, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2→49.33 Å / Num. obs: 271538 / % possible obs: 99 % / Redundancy: 4.6 % / CC_1/2: 0.995 / R_rim(I) all: 0.17 / Net I/σ(I): 5.3
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 36741 / CC_1/2: 0.484 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0230	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6I33

6i33

Resolution: 2→49.33 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.955 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24047	13576	5 %	RANDOM
R_work	0.215	-	-	-
obs	0.21627	257933	98.99 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å

Displacement parameters

B_iso mean: 47.125 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.71 Å²	0 Å²	2.96 Å²
2-	-	0.75 Å²	0 Å²
3-	-	-	1.1 Å²

Refinement step

Cycle: 1 / Resolution: 2→49.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	29750	0	158	1024	30932

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.014	30560
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	27388
X-RAY DIFFRACTION	r_angle_refined_deg	1.341	1.659	41354
X-RAY DIFFRACTION	r_angle_other_deg	1.445	1.637	64346
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.733	5	3808
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.214	21.905	1596
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.713	15	5210
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.064	15	216
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	3949
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	34432
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	5456
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	1.134	1.826	15262
X-RAY DIFFRACTION	r_mcbond_other	1.134	1.826	15263
X-RAY DIFFRACTION	r_mcangle_it	1.802	2.732	19060
X-RAY DIFFRACTION	r_mcangle_other	1.803	2.733	19061
X-RAY DIFFRACTION	r_scbond_it	1.453	2.021	15298
X-RAY DIFFRACTION	r_scbond_other	1.45	2.02	15295
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.252	2.958	22292
X-RAY DIFFRACTION	r_long_range_B_refined	5.241	22.28	34499
X-RAY DIFFRACTION	r_long_range_B_other	5.24	22.125	34371
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	32331	0.08
1	2	B	32331	0.08
2	1	A	32761	0.06
2	2	C	32761	0.06
3	1	A	32246	0.08
3	2	D	32246	0.08
4	1	B	32350	0.07
4	2	C	32350	0.07
5	1	B	32622	0.06
5	2	D	32622	0.06
6	1	C	32292	0.07
6	2	D	32292	0.07

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.402	991	-
R_work	0.389	18832	-
obs	-	-	98.22 %

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	0.7773	0.0784	-0.0804	0.9822	-0.0686	0.6656	0.0471	0.1019	0.0294	-0.0684	0.0163	-0.1204	-0.0295	0.1015	-0.0634	0.2905	0.0137	-0.2513	0.0333	-0.0209	0.2746	18.519	-23.069	-4.741
2	1.1942	0.1102	0.4458	1.1517	-0.3576	1.6111	0.0229	0.2624	-0.0795	-0.2702	0.0751	0.1572	0.1117	-0.1094	-0.0979	0.3515	0.001	-0.3056	0.0878	-0.0175	0.2771	-1.86	-33.866	-13.723
3	0.8591	-0.1867	-0.2551	2.6832	0.4623	0.8248	0.1136	0.0724	0.185	-0.0571	-0.0612	0.4181	-0.1654	-0.183	-0.0524	0.2477	0.042	-0.1553	0.0475	0.0345	0.3292	-14.941	-15.471	7.432
4	3.568	0.7227	-2.8556	1.1469	-0.3339	3.4355	0.1094	-0.1395	0.1429	0.2304	-0.0405	0.1115	-0.2672	-0.0505	-0.069	0.3486	0.0427	-0.1679	0.0299	-0.0187	0.321	-2.54	-2.519	12.287
5	0.7518	0.0023	0.0711	1.1022	-0.1342	0.8133	0.0691	-0.27	0.0019	0.4517	-0.0174	-0.1604	0.0146	0.141	-0.0518	0.5387	-0.0015	-0.3473	0.1736	-0.0319	0.253	20.934	-32.122	37.749
6	1.0464	-0.0892	-0.0254	2.9436	0.3299	1.1092	0.0507	-0.2773	-0.1712	0.472	0.0393	0.0023	0.1814	0.0024	-0.0901	0.46	-0.0035	-0.2672	0.1492	0.0628	0.2083	11.243	-46.284	34.344
7	0.6667	0.2164	0.1095	1.0044	-0.0677	0.6867	0.0727	-0.2769	0.1054	0.471	-0.0461	-0.2237	-0.1167	0.2082	-0.0265	0.5382	-0.0541	-0.363	0.2251	-0.0745	0.3164	28.615	-19.297	38.547
8	1.4603	0.0868	0.6303	4.5534	-1.3131	1.5763	-0.0489	-0.2718	0.2803	0.5577	0.1495	0.2225	-0.295	-0.1815	-0.1007	0.5304	0.0178	-0.1422	0.1717	-0.1255	0.3186	3.335	-2.825	33.871
9	0.7556	-0.0973	-0.0291	0.9743	0.0203	0.7196	0.0619	-0.1545	0.031	0.1016	-0.0006	0.0387	-0.0094	-0.0365	-0.0613	0.2974	-0.0317	-0.2532	0.0356	0.0124	0.2524	-26.223	34.184	105.116
10	1.9314	-2.1645	2.0895	2.4509	-2.3599	2.2897	0.0307	-0.1159	-0.0827	-0.0657	0.0576	0.0253	0.1288	-0.0656	-0.0884	0.4201	0.0543	-0.0745	0.3158	0.087	0.403	-31.113	20.662	114.632
11	1.1008	0.3746	-0.4394	1.4915	-0.488	0.6303	0.1662	-0.136	0.1316	0.004	-0.1087	-0.3483	-0.1305	0.1919	-0.0576	0.337	-0.0459	-0.2185	0.0599	-0.0299	0.4144	-2.715	40.649	92.41
12	3.6328	-0.9403	-2.9585	1.2534	0.5208	3.2139	0.1011	0.1579	0.1668	-0.2638	-0.0721	-0.1122	-0.2707	0.0105	-0.029	0.361	-0.0348	-0.1656	0.0313	0.022	0.3114	-10.967	57.161	85.608
13	0.593	0.1868	-0.0086	1.0952	-0.1766	1.2116	0.0684	-0.0336	0.1416	-0.1629	0.0416	0.5637	-0.1768	-0.3937	-0.1101	0.3826	0.0544	-0.3418	0.2164	0.0533	0.541	-53.695	43.022	77.343
14	0.9912	-0.0965	0.1626	1.7152	0.2035	0.9067	0.1102	0.3254	-0.1338	-0.5722	-0.0473	0.0419	0.0898	0.0427	-0.063	0.5743	0.0515	-0.3009	0.1464	-0.0313	0.2376	-25.674	17.783	57.65
15	0.7724	-0.2426	0.1505	1.0333	0.0296	0.6636	0.095	0.2653	0.0895	-0.5246	-0.0707	0.244	-0.1195	-0.1588	-0.0243	0.5828	0.0679	-0.3759	0.179	0.0602	0.3217	-42.008	40.428	59.186
16	1.6424	-0.1781	0.571	4.949	1.6221	1.6595	-0.0115	0.2497	0.2307	-0.6174	0.1109	-0.1466	-0.2859	0.2222	-0.0994	0.5174	-0.0052	-0.1405	0.1603	0.1326	0.3176	-16.725	56.928	63.981

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	49 - 591
2	X-RAY DIFFRACTION	2	A	592 - 823
3	X-RAY DIFFRACTION	3	A	824 - 958
4	X-RAY DIFFRACTION	4	A	959 - 1005
5	X-RAY DIFFRACTION	5	B	51 - 340
6	X-RAY DIFFRACTION	6	B	341 - 506
7	X-RAY DIFFRACTION	7	B	507 - 940
8	X-RAY DIFFRACTION	8	B	941 - 1004
9	X-RAY DIFFRACTION	9	C	49 - 781
10	X-RAY DIFFRACTION	10	C	782 - 790
11	X-RAY DIFFRACTION	11	C	794 - 958
12	X-RAY DIFFRACTION	12	C	959 - 1005
13	X-RAY DIFFRACTION	13	D	51 - 130
14	X-RAY DIFFRACTION	14	D	131 - 506
15	X-RAY DIFFRACTION	15	D	507 - 940
16	X-RAY DIFFRACTION	16	D	941 - 1004

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 6 types, 1042 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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