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- PDB-6i34: Crystal structure of Neanderthal glycine decarboxylase (P-protein) -

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Basic information

Entry
Database: PDB / ID: 6i34
TitleCrystal structure of Neanderthal glycine decarboxylase (P-protein)
ComponentsNeanderthal Glycine decarboxylase
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 decarboxylation via glycine cleavage system / glycine cleavage complex / 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 decarboxylation via glycine cleavage system / glycine cleavage complex / 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
DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Glycine dehydrogenase (decarboxylating), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens neanderthalensis (Neandertal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: Neanderthal Glycine decarboxylase
B: Neanderthal Glycine decarboxylase
C: Neanderthal Glycine decarboxylase
D: Neanderthal Glycine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)440,84729
Polymers438,1854
Non-polymers2,66225
Water24,4821359
1
A: Neanderthal Glycine decarboxylase
B: Neanderthal Glycine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,35614
Polymers219,0922
Non-polymers1,26312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11160 Å2
ΔGint13 kcal/mol
Surface area59360 Å2
MethodPISA
2
C: Neanderthal Glycine decarboxylase
D: Neanderthal Glycine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,49215
Polymers219,0922
Non-polymers1,39913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint15 kcal/mol
Surface area58930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.873, 124.381, 201.304
Angle α, β, γ (deg.)90.00, 98.57, 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: _ / Refine code: _

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
13LEULEUPROPROAA52 - 10049 - 961
23LEULEUPROPRODD52 - 10049 - 961
14ARGARGPROPROBB51 - 10048 - 961
24ARGARGPROPROCC51 - 10048 - 961
15LEULEUPROPROBB52 - 10039 - 960
25LEULEUPROPRODD52 - 10039 - 960
16LEULEUPROPROCC52 - 10049 - 961
26LEULEUPROPRODD52 - 10049 - 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
Neanderthal Glycine decarboxylase


Mass: 109546.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens neanderthalensis (Neandertal)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P23378*PLUS, glycine dehydrogenase (aminomethyl-transferring)

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Non-polymers , 5 types, 1384 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1359 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: ID30B / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→47.9 Å / Num. obs: 245944 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / CC1/2: 0.993 / Rrim(I) all: 0.192 / Net I/σ(I): 5.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.64 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I33

6i33


Resolution: 2.1→47.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 12259 5 %RANDOM
Rwork0.216 ---
obs0.218 233556 99.8 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 36.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å20 Å21.66 Å2
2--0.85 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29751 0 169 1359 31279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01430604
X-RAY DIFFRACTIONr_bond_other_d0.0010.01727416
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.65941390
X-RAY DIFFRACTIONr_angle_other_deg1.6191.63864404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14953815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46421.9251600
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.541155209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.27715215
X-RAY DIFFRACTIONr_chiral_restr0.1310.23952
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0234416
X-RAY DIFFRACTIONr_gen_planes_other0.0090.025480
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_it1.6091.33115266
X-RAY DIFFRACTIONr_mcbond_other1.6081.33115265
X-RAY DIFFRACTIONr_mcangle_it2.4061.98819079
X-RAY DIFFRACTIONr_mcangle_other2.4061.98819080
X-RAY DIFFRACTIONr_scbond_it2.5511.61215338
X-RAY DIFFRACTIONr_scbond_other2.5511.61215338
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8172.30422312
X-RAY DIFFRACTIONr_long_range_B_refined6.1216.3333395
X-RAY DIFFRACTIONr_long_range_B_other6.11316.15233224
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)
11A314650.07
12B314650.07
21A320150.05
22C320150.05
31A315750.07
32D315750.07
41B315140.07
42C315140.07
51B318370.06
52D318370.06
61C315400.06
62D315400.06
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 853 -
Rwork0.348 17305 -
obs--99.93 %
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)
10.63490.048-0.00770.7242-0.05550.54630.02950.0890.0475-0.04550.01580.0228-0.00940.0202-0.04520.23820.0108-0.13760.01370.00050.09097.783-25.508-4.126
20.56410.05930.12850.9382-0.06790.70530.0454-0.2090.05310.3765-0.0053-0.11670.00060.1004-0.04010.4645-0.0001-0.20680.1617-0.04350.109721.171-28.58637.62
30.6375-0.03120.02970.71540.04990.5390.0488-0.09690.04220.0405-0.0008-0.0145-0.0044-0.0161-0.04790.2395-0.0178-0.13630.01550.00080.0912-22.81535.054103.647
40.5822-0.07260.20110.85490.01030.70540.07380.180.0266-0.3492-0.03240.11430.0271-0.0378-0.04130.45780.0231-0.20510.13630.03030.1075-36.06331.90161.832
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 1005
2X-RAY DIFFRACTION2B51 - 1004
3X-RAY DIFFRACTION3C49 - 1005
4X-RAY DIFFRACTION4D52 - 1004

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