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- PDB-1wyv: Crystal structure of glycine decarboxylase (P-protein) of the gly... -

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Basic information

Entry
Database: PDB / ID: 1wyv
TitleCrystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form
Components
  • glycine dehydrogenase (decarboxylating) subunit 1
  • glycine dehydrogenase subunit 2 (P-protein)
KeywordsOXIDOREDUCTASE / ALPHA(2)BETA(2) TETRAMER / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


glycine dehydrogenase (aminomethyl-transferring) / glycine dehydrogenase (decarboxylating) activity / glycine decarboxylation via glycine cleavage system / glycine cleavage complex / nucleoside metabolic process / glycine binding / pyridoxal phosphate binding / cytosol
Similarity search - Function
Translocated Intimin Receptor; Chain T / Translocated Intimin Receptor; Chain T - #10 / Probable glycine dehydrogenase (decarboxylating) subunit 1 / Probable glycine dehydrogenase (decarboxylating) subunit 2 / Glycine cleavage system P protein / : / : / Glycine cleavage system P-protein / Glycine dehydrogenase, C-terminal domain / Other non-globular ...Translocated Intimin Receptor; Chain T / Translocated Intimin Receptor; Chain T - #10 / Probable glycine dehydrogenase (decarboxylating) subunit 1 / Probable glycine dehydrogenase (decarboxylating) subunit 2 / Glycine cleavage system P protein / : / : / Glycine cleavage system P-protein / Glycine dehydrogenase, C-terminal domain / Other non-globular / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Special / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(AMINOOXY)ACETIC ACID / PYRIDOXAL-5'-PHOSPHATE / : / : / Probable glycine dehydrogenase (decarboxylating) subunit 2 / Probable glycine dehydrogenase (decarboxylating) subunit 1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsNakai, T. / Nakagawa, N. / Maoka, N. / Masui, R. / Kuramitsu, S. / Kamiya, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Embo J. / Year: 2005
Title: Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia
Authors: Nakai, T. / Nakagawa, N. / Maoka, N. / Masui, R. / Kuramitsu, S. / Kamiya, N.
History
DepositionFeb 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycine dehydrogenase (decarboxylating) subunit 1
B: glycine dehydrogenase subunit 2 (P-protein)
C: glycine dehydrogenase (decarboxylating) subunit 1
D: glycine dehydrogenase subunit 2 (P-protein)
E: glycine dehydrogenase (decarboxylating) subunit 1
F: glycine dehydrogenase subunit 2 (P-protein)
G: glycine dehydrogenase (decarboxylating) subunit 1
H: glycine dehydrogenase subunit 2 (P-protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,16416
Polymers399,8118
Non-polymers1,3538
Water21,4741192
1
A: glycine dehydrogenase (decarboxylating) subunit 1
B: glycine dehydrogenase subunit 2 (P-protein)
C: glycine dehydrogenase (decarboxylating) subunit 1
D: glycine dehydrogenase subunit 2 (P-protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,5828
Polymers199,9064
Non-polymers6764
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41640 Å2
ΔGint-236 kcal/mol
Surface area52330 Å2
MethodPISA
2
E: glycine dehydrogenase (decarboxylating) subunit 1
F: glycine dehydrogenase subunit 2 (P-protein)
G: glycine dehydrogenase (decarboxylating) subunit 1
H: glycine dehydrogenase subunit 2 (P-protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,5828
Polymers199,9064
Non-polymers6764
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41710 Å2
ΔGint-242 kcal/mol
Surface area52380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.173, 166.317, 190.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is an alpha(2)beta(2) tetramer. The asymmetric unit contains two sets of the assembly (chains A-D and E-H).

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Components

#1: Protein
glycine dehydrogenase (decarboxylating) subunit 1 / P-protein of the glycine cleavage system subunit 1


Mass: 47168.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: GCSA / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)
References: GenBank: 55771907, UniProt: Q5SKW8*PLUS, glycine dehydrogenase (aminomethyl-transferring)
#2: Protein
glycine dehydrogenase subunit 2 (P-protein) / P-protein of the glycine cleavage system subunit 2


Mass: 52784.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: GCSB / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)
References: GenBank: 55771908, UniProt: Q5SKW7*PLUS, glycine dehydrogenase (aminomethyl-transferring)
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical
ChemComp-AOA / (AMINOOXY)ACETIC ACID


Mass: 91.066 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1192 / 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: 2.69 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, lithium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 29, 2004
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 167358 / Num. obs: 166371 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 16
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3.1 / Num. unique all: 16003 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: P-PROTEIN IN THE HOLO-FORM

Resolution: 2.4→47.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4234196.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 8338 5 %RANDOM
Rwork0.188 ---
all0.19 166280 --
obs0.19 165655 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.302 Å2 / ksol: 0.353867 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.85 Å20 Å20 Å2
2---4.33 Å20 Å2
3----3.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28132 0 84 1192 29408
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 1393 5.1 %
Rwork0.234 25756 -
obs-27149 99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4PLP.PARAM
X-RAY DIFFRACTION5AOA.PARAM

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