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- PDB-6i33: Crystal structure of human glycine decarboxylase (P-protein) -

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Basic information

Entry
Database: PDB / ID: 6i33
TitleCrystal structure of human glycine decarboxylase (P-protein)
ComponentsGlycine dehydrogenase (decarboxylating), mitochondrial
KeywordsOXIDOREDUCTASE / mitochondrial / glycine decarboxylase / glycine cleavage system P-protein
Function / homology
Function and homology information


response to methylamine / response to lipoic acid / glycine dehydrogenase (aminomethyl-transferring) / pyridoxal binding / 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 / glycine dehydrogenase (aminomethyl-transferring) / pyridoxal binding / 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
BICARBONATE ION / PYRIDOXAL-5'-PHOSPHATE / Glycine dehydrogenase (decarboxylating), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 15, 2020Group: Advisory / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.2Jan 24, 2024Group: 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_ncs_dom_lim
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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,13814
Polymers219,0242
Non-polymers1,11412
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10980 Å2
ΔGint14 kcal/mol
Surface area57710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.810, 123.510, 99.510
Angle α, β, γ (deg.)90.00, 97.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 51 - 1004 / Label seq-ID: 8 - 961

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 109512.203 Da / Num. of mol.: 2
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)
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
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: MASSIF-3 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→46.1 Å / Num. obs: 90460 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 4.5 % / CC1/2: 0.99 / Rrim(I) all: 0.079 / Net I/σ(I): 12.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 13232 / CC1/2: 0.74 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LHD

4lhd


Resolution: 2.3→46.08 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23549 4521 5 %RANDOM
Rwork0.21168 ---
obs0.2129 85899 99.18 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.399 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å21.29 Å2
2---1.97 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: 1 / Resolution: 2.3→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14617 0 70 165 14852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915007
X-RAY DIFFRACTIONr_bond_other_d00.0213885
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.96220292
X-RAY DIFFRACTIONr_angle_other_deg3.749332247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48251867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24223.735672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.149152552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.87315105
X-RAY DIFFRACTIONr_chiral_restr0.0840.22234
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116620
X-RAY DIFFRACTIONr_gen_planes_other0.0160.022997
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_it0.391.0147492
X-RAY DIFFRACTIONr_mcbond_other0.391.0137491
X-RAY DIFFRACTIONr_mcangle_it0.7021.5199351
X-RAY DIFFRACTIONr_mcangle_other0.7021.5199352
X-RAY DIFFRACTIONr_scbond_it0.7181.1027515
X-RAY DIFFRACTIONr_scbond_other0.7181.1027515
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8131.61410942
X-RAY DIFFRACTIONr_long_range_B_refined6.2512.34416600
X-RAY DIFFRACTIONr_long_range_B_other6.24912.28316586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 60176 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 333 -
Rwork0.346 6345 -
obs--99.69 %
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)
10.78730.0642-0.17420.9383-0.09680.74750.05010.02550.0789-0.04920.02720.0486-0.01510.0025-0.07730.0460.0224-0.11670.6882-0.01370.380514.606-23.91-53.474
20.71340.0575-0.06331.105-0.08970.86060.0495-0.36090.07910.46740.0083-0.117-0.01820.1877-0.05790.26860.0137-0.20461.0267-0.07560.380327.432-27.193-12.57
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 1005
2X-RAY DIFFRACTION2B51 - 1004

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