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- PDB-1dxm: Reduced form of the H protein from glycine decarboxylase complex -

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Basic information

Entry
Database: PDB / ID: 1dxm
TitleReduced form of the H protein from glycine decarboxylase complex
ComponentsH PROTEIN
KeywordsOXIDOREDUCTASES(ACTING ON CH-NH2 DONOR) / GLYCINE DECARBOXYLASE / MITOCHONDRIA
Function / homology
Function and homology information


glycine decarboxylation via glycine cleavage system / glycine cleavage complex / mitochondrial matrix
Similarity search - Function
Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif ...Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DIHYDROLIPOIC ACID / Glycine cleavage system H protein, mitochondrial
Similarity search - Component
Biological speciesPISUM SATIVUM (garden pea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFaure, M. / Cohen-Addad, C. / Neuburger, M. / Douce, R.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: Interaction between the Lipoamide-Containing H-Protein and the Lipoamide Dehydrogenase (L-Protein) of the Glycine Decarboxylase Multienzyme System. 2. Crystal Structure of H- and L-Proteins
Authors: Faure, M. / Bourguignon, J. / Neuburger, M. / Macherel, D. / Sieker, L. / Ober, R. / Kahn, R. / Cohen-Addad, C. / Douce, R.
#1: Journal: Biochimie / Year: 1997
Title: Structural Studies of the Glycine Decarboxylase Complex from Pea Leaf Mitochondria
Authors: Cohen-Addad, C. / Faure, M. / Neuburger, M. / Ober, R. / Sieker, L. / Bourguignon, J. / Macherel, D. / Douce, R.
#2: Journal: Nat.Struct.Biol. / Year: 1995
Title: The Lipoamide Arm in the Glycine Decarboxylase is not Freely Swinging
Authors: Cohen-Addad, C. / Pares, S. / Sieker, L. / Neuburger, M. / Douce, R.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Refined Structures at 2 and 2.2 A Resolution of Two Forms of the H-Protein, a Lipoamide-Containing Protein of the Glycine Decarboxylase Complex
Authors: Pares, S. / Cohen-Addad, C. / Sieker, L. / Neuburger, M. / Douce, R.
History
DepositionJan 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 6, 2023Group: 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_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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H PROTEIN
B: H PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3424
Polymers27,9252
Non-polymers4172
Water2,612145
1
A: H PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1712
Polymers13,9621
Non-polymers2081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: H PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1712
Polymers13,9621
Non-polymers2081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.410, 56.410, 135.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.39443, 0.54761, 0.73794), (0.91369, -0.3193, -0.25143), (0.09794, 0.77342, -0.62629)
Vector: -0.16918, -0.57433, 0.15324)
DetailsBIOLOGICAL_UNIT: MONOMERTHE GLYCINE CLEAVAGE SYSTEM IS COMPOSED OF FOUR PROTEINS:P, T, L, AND H. THE H CHAIN WAS STUDIED HERE. THIS COMPONENTSHUTTLES THE METHYLAMINE GROUP OF GLYCINE FROM THE P PROTEINTO THE T PROTEIN. THE H CHAIN CONTAINS A COVALENTLY-BOUNDLIPOYL COFACTOR.

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Components

#1: Protein H PROTEIN / GLYCINE CLEAVAGE SYSTEM H PROTEIN


Mass: 13962.464 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PISUM SATIVUM (garden pea) / Organ: LEAF / Organelle: MITOCHONDRIA / Plasmid: PET-HM / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16048
#2: Chemical ChemComp-RED / DIHYDROLIPOIC ACID


Mass: 208.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growpH: 5.2
Details: 50 % AMMONIUM SULFATE, 100 MM TRIS MALEATE PH 5.2, 2 MM TCEP (TRIS CARBOXYETHYL PHOSPHINE)
Crystal grow
*PLUS
Temperature: 8 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate1reservoir
210 mMTCEP1reservoir
3100 mMTris maleate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorDetector: IMAGE PLATE / Date: Dec 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 7808 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 47.6 Å2 / Rsym value: 0.11 / Net I/σ(I): 4.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3 / Rsym value: 0.24 / % possible all: 98.3
Reflection
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 98.3 % / Rmerge(I) obs: 0.24

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Processing

Software
NameVersionClassification
CNS0.5refinement
XDSdata reduction
SCALAdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HPC

1hpc


Resolution: 2.6→40 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1374190.82 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.26 410 5.3 %RANDOM
Rwork0.204 ---
obs0.204 7740 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48 Å2 / ksol: 0.358993 e/Å3
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å2-2.07 Å20 Å2
2--3.41 Å20 Å2
3----6.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 22 145 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 60 4.7 %
Rwork0.283 1217 -
obs--96.4 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.207 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17

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