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

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Basic information

Entry
Database: PDB / ID: 6i35
TitleCrystal structure of human glycine decarboxylase (P-protein) bound with pyridoxyl-glycine-5'-monophosphate
ComponentsGlycine dehydrogenase (decarboxylating), mitochondrialGlycine dehydrogenase (decarboxylating)
KeywordsOXIDOREDUCTASE / 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 cleavage complex / glycine decarboxylation via glycine cleavage system / glycine binding ...response to methylamine / response to lipoic acid / pyridoxal binding / glycine dehydrogenase (aminomethyl-transferring) / glycine dehydrogenase (decarboxylating) activity / glycine catabolic process / Glycine degradation / glycine cleavage complex / glycine decarboxylation via glycine cleavage system / glycine binding / cellular response to leukemia inhibitory factor / pyridoxal phosphate binding / electron transfer activity / lyase activity / mitochondrial matrix / protein homodimerization activity / mitochondrion / nucleoplasm / plasma membrane
Similarity search - Function
Glycine dehydrogenase (decarboxylating) / Glycine cleavage system P protein / : / : / Glycine cleavage system P-protein / Glycine dehydrogenase, C-terminal domain / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
BICARBONATE ION / DI(HYDROXYETHYL)ETHER / Chem-PLG / Glycine dehydrogenase (decarboxylating), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVan Laer, B. / Kapp, U. / Leonard, G. / Mueller-Dieckmann, C.
CitationJournal: 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
DepositionNov 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine dehydrogenase (decarboxylating), mitochondrial
B: Glycine dehydrogenase (decarboxylating), mitochondrial
C: Glycine dehydrogenase (decarboxylating), mitochondrial
D: Glycine dehydrogenase (decarboxylating), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)440,46822
Polymers438,0494
Non-polymers2,41918
Water18,4471024
1
A: Glycine dehydrogenase (decarboxylating), mitochondrial
B: Glycine dehydrogenase (decarboxylating), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,20411
Polymers219,0242
Non-polymers1,1809
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-3 kcal/mol
Surface area57290 Å2
MethodPISA
2
C: Glycine dehydrogenase (decarboxylating), mitochondrial
D: Glycine dehydrogenase (decarboxylating), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,26411
Polymers219,0242
Non-polymers1,2399
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9810 Å2
ΔGint6 kcal/mol
Surface area57330 Å2
MethodPISA
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 number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGPROPROAA51 - 10048 - 961
21ARGARGPROPROBB51 - 10048 - 961
12ALAALAMETMETAA49 - 10056 - 962
22ALAALAMETMETCC49 - 10056 - 962
13ARGARGPROPROAA51 - 10048 - 961
23ARGARGPROPRODD51 - 10048 - 961
14ARGARGPROPROBB51 - 10048 - 961
24ARGARGPROPROCC51 - 10048 - 961
15ARGARGPROPROBB51 - 10048 - 961
25ARGARGPROPRODD51 - 10048 - 961
16ARGARGPROPROCC51 - 10048 - 961
26ARGARGPROPRODD51 - 10048 - 961

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glycine dehydrogenase (decarboxylating), mitochondrial / Glycine dehydrogenase (decarboxylating) / 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 / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


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 / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1024 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→49.33 Å / Num. obs: 271538 / % possible obs: 99 % / Redundancy: 4.6 % / CC1/2: 0.995 / Rrim(I) all: 0.17 / Net I/σ(I): 5.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 36741 / CC1/2: 0.484 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I33

6i33


Resolution: 2→49.33 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.24047 13576 5 %RANDOM
Rwork0.215 ---
obs0.21627 257933 98.99 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 47.125 Å2
Baniso -1Baniso -2Baniso -3
1--2.71 Å20 Å22.96 Å2
2--0.75 Å20 Å2
3---1.1 Å2
Refinement stepCycle: 1 / Resolution: 2→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29750 0 158 1024 30932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01430560
X-RAY DIFFRACTIONr_bond_other_d0.0010.01727388
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.65941354
X-RAY DIFFRACTIONr_angle_other_deg1.4451.63764346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73353808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21421.9051596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.713155210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.06415216
X-RAY DIFFRACTIONr_chiral_restr0.0820.23949
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0234432
X-RAY DIFFRACTIONr_gen_planes_other0.0110.025456
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1341.82615262
X-RAY DIFFRACTIONr_mcbond_other1.1341.82615263
X-RAY DIFFRACTIONr_mcangle_it1.8022.73219060
X-RAY DIFFRACTIONr_mcangle_other1.8032.73319061
X-RAY DIFFRACTIONr_scbond_it1.4532.02115298
X-RAY DIFFRACTIONr_scbond_other1.452.0215295
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2522.95822292
X-RAY DIFFRACTIONr_long_range_B_refined5.24122.2834499
X-RAY DIFFRACTIONr_long_range_B_other5.2422.12534371
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A323310.08
12B323310.08
21A327610.06
22C327610.06
31A322460.08
32D322460.08
41B323500.07
42C323500.07
51B326220.06
52D326220.06
61C322920.07
62D322920.07
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 991 -
Rwork0.389 18832 -
obs--98.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.77730.0784-0.08040.9822-0.06860.66560.04710.10190.0294-0.06840.0163-0.1204-0.02950.1015-0.06340.29050.0137-0.25130.0333-0.02090.274618.519-23.069-4.741
21.19420.11020.44581.1517-0.35761.61110.02290.2624-0.0795-0.27020.07510.15720.1117-0.1094-0.09790.35150.001-0.30560.0878-0.01750.2771-1.86-33.866-13.723
30.8591-0.1867-0.25512.68320.46230.82480.11360.07240.185-0.0571-0.06120.4181-0.1654-0.183-0.05240.24770.042-0.15530.04750.03450.3292-14.941-15.4717.432
43.5680.7227-2.85561.1469-0.33393.43550.1094-0.13950.14290.2304-0.04050.1115-0.2672-0.0505-0.0690.34860.0427-0.16790.0299-0.01870.321-2.54-2.51912.287
50.75180.00230.07111.1022-0.13420.81330.0691-0.270.00190.4517-0.0174-0.16040.01460.141-0.05180.5387-0.0015-0.34730.1736-0.03190.25320.934-32.12237.749
61.0464-0.0892-0.02542.94360.32991.10920.0507-0.2773-0.17120.4720.03930.00230.18140.0024-0.09010.46-0.0035-0.26720.14920.06280.208311.243-46.28434.344
70.66670.21640.10951.0044-0.06770.68670.0727-0.27690.10540.471-0.0461-0.2237-0.11670.2082-0.02650.5382-0.0541-0.3630.2251-0.07450.316428.615-19.29738.547
81.46030.08680.63034.5534-1.31311.5763-0.0489-0.27180.28030.55770.14950.2225-0.295-0.1815-0.10070.53040.0178-0.14220.1717-0.12550.31863.335-2.82533.871
90.7556-0.0973-0.02910.97430.02030.71960.0619-0.15450.0310.1016-0.00060.0387-0.0094-0.0365-0.06130.2974-0.0317-0.25320.03560.01240.2524-26.22334.184105.116
101.9314-2.16452.08952.4509-2.35992.28970.0307-0.1159-0.0827-0.06570.05760.02530.1288-0.0656-0.08840.42010.0543-0.07450.31580.0870.403-31.11320.662114.632
111.10080.3746-0.43941.4915-0.4880.63030.1662-0.1360.13160.004-0.1087-0.3483-0.13050.1919-0.05760.337-0.0459-0.21850.0599-0.02990.4144-2.71540.64992.41
123.6328-0.9403-2.95851.25340.52083.21390.10110.15790.1668-0.2638-0.0721-0.1122-0.27070.0105-0.0290.361-0.0348-0.16560.03130.0220.3114-10.96757.16185.608
130.5930.1868-0.00861.0952-0.17661.21160.0684-0.03360.1416-0.16290.04160.5637-0.1768-0.3937-0.11010.38260.0544-0.34180.21640.05330.541-53.69543.02277.343
140.9912-0.09650.16261.71520.20350.90670.11020.3254-0.1338-0.5722-0.04730.04190.08980.0427-0.0630.57430.0515-0.30090.1464-0.03130.2376-25.67417.78357.65
150.7724-0.24260.15051.03330.02960.66360.0950.26530.0895-0.5246-0.07070.244-0.1195-0.1588-0.02430.58280.0679-0.37590.1790.06020.3217-42.00840.42859.186
161.6424-0.17810.5714.9491.62211.6595-0.01150.24970.2307-0.61740.1109-0.1466-0.28590.2222-0.09940.5174-0.0052-0.14050.16030.13260.3176-16.72556.92863.981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 591
2X-RAY DIFFRACTION2A592 - 823
3X-RAY DIFFRACTION3A824 - 958
4X-RAY DIFFRACTION4A959 - 1005
5X-RAY DIFFRACTION5B51 - 340
6X-RAY DIFFRACTION6B341 - 506
7X-RAY DIFFRACTION7B507 - 940
8X-RAY DIFFRACTION8B941 - 1004
9X-RAY DIFFRACTION9C49 - 781
10X-RAY DIFFRACTION10C782 - 790
11X-RAY DIFFRACTION11C794 - 958
12X-RAY DIFFRACTION12C959 - 1005
13X-RAY DIFFRACTION13D51 - 130
14X-RAY DIFFRACTION14D131 - 506
15X-RAY DIFFRACTION15D507 - 940
16X-RAY DIFFRACTION16D941 - 1004

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