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- PDB-1hpc: REFINED STRUCTURES AT 2 ANGSTROMS AND 2.2 ANGSTROMS OF THE TWO FO... -

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Basic information

Entry
Database: PDB / ID: 1hpc
TitleREFINED STRUCTURES AT 2 ANGSTROMS AND 2.2 ANGSTROMS OF THE TWO FORMS OF THE H-PROTEIN, A LIPOAMIDE-CONTAINING PROTEIN OF THE GLYCINE DECARBOXYLASE
ComponentsH PROTEIN OF THE GLYCINE CLEAVAGE SYSTEM
KeywordsTRANSIT PEPTIDE
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
LIPOIC ACID / 5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid / Glycine cleavage system H protein, mitochondrial
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsPares, S. / Cohen-Addad, C. / Sieker, L. / Neuburger, M. / Douce, R.
Citation
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.C. / Neuburger, M. / Douce, R.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: The Lipoamide Arm in the Glycine Decarboxylase Complex is not Freely Swinging
Authors: Cohen-Addad, C. / Pares, S. / Sieker, L. / Neuburger, M. / Douce, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: X-Ray Structure Determination at 2.6 Angstroms Resolution of a Lipoate-Containing Protein: The H-Protein of the Glycine Decarboxylase Complex from Pea Leaves
Authors: Pares, S. / Cohen-Addad, C. / Sieker, L. / Neuburger, M. / Douce, R.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallographic Data for H-Protein from the Glycine Decarboxylase Complex
Authors: Sieker, L. / Cohen-Addad, C. / Neuburger, M. / Douce, R.
#4: Journal: Biochem.J. / Year: 1990
Title: Cdna Cloning, Primary Structure and Gene Expression for H-Protein, a Component of the Glycine-Cleavage System (Glycine Decarboxylase) of Pea (Pisum Sativum) Leaf Mitochondria
Authors: Macherel, D. / Lebrun, M. / Gagnon, J. / Neuburger, M. / Douce, R.
History
DepositionFeb 17, 1994Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 5, 2011Group: Non-polymer description
Revision 1.4Apr 16, 2014Group: Derived calculations
Revision 1.5Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H PROTEIN OF THE GLYCINE CLEAVAGE SYSTEM
B: H PROTEIN OF THE GLYCINE CLEAVAGE SYSTEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3384
Polymers27,9252
Non-polymers4132
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.300, 57.300, 136.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.3895, 0.566, 0.726), (0.9138, -0.3, -0.25), (0.0714, 0.767, -0.637)
Vector: 7.29, -28.7, 22.17)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein H PROTEIN OF THE GLYCINE CLEAVAGE SYSTEM


Mass: 13962.464 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea)
References: UniProt: P16048, glycine dehydrogenase (aminomethyl-transferring)
#2: Chemical ChemComp-LPB / 5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid


Mass: 206.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O2S2
#3: Chemical ChemComp-LPA / LIPOIC ACID / 5-[(3R)-1,2-dithiolan-3-yl]pentanoic acid


Mass: 206.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
Temperature: 281 K / pH: 5.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate11
20.1 MTris naleate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 17031 / % possible obs: 92 %
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 87067 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 80 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.185 -
obs0.185 16839
Displacement parametersBiso mean: 23 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 22 206 2194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_planar_d25.8

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