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- PDB-3klr: Bovine H-protein at 0.88 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 3klr
TitleBovine H-protein at 0.88 angstrom resolution
ComponentsGlycine cleavage system H protein
KeywordsOXIDOREDUCTASE / antiparallel beta sheet / beta sandwich
Function / homology
Function and homology information


Glycine degradation / Glyoxylate metabolism and glycine degradation / glycine cleavage complex / glycine decarboxylation via glycine cleavage system / mitochondrion / cytoplasm
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
Glycine cleavage system H protein, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.88 Å
AuthorsHigashiura, A. / Kurakane, T. / Matsuda, M. / Suzuki, M. / Inaka, K. / Sato, M. / Tanaka, H. / Fujiwara, K. / Nakagawa, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: High-resolution X-ray crystal structure of bovine H-protein at 0.88 A resolution
Authors: Higashiura, A. / Kurakane, T. / Matsuda, M. / Suzuki, M. / Inaka, K. / Sato, M. / Kobayashi, T. / Tanaka, T. / Tanaka, H. / Fujiwara, K. / Nakagawa, A.
History
DepositionNov 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycine cleavage system H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1434
Polymers13,8581
Non-polymers2843
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.584, 41.295, 43.124
Angle α, β, γ (deg.)90.000, 91.180, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-388-

HOH

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Components

#1: Protein Glycine cleavage system H protein /


Mass: 13858.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20821
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.72 Å3/Da / Density % sol: 54.72 % / Mosaicity: 0.414 °
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 2.0M ammonium sulfate, 0.1M sodium citrate, pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2007
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.88→45 Å / Num. obs: 115668 / % possible obs: 98.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 6.95 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.876 / Net I/σ(I): 19.5
Reflection shellResolution: 0.88→0.89 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.426 / Num. unique all: 3698 / Χ2: 1.089 / % possible all: 95.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
MOLREPphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HPC

1hpc


Resolution: 0.88→45 Å / Num. parameters: 12878 / Num. restraintsaints: 16868 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(I): 4 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1311 --RANDOM
Rwork0.1117 ---
obs-109877 93.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso max: 69.19 Å2 / Biso mean: 14.628 Å2 / Biso min: 5.54 Å2
Refinement stepCycle: LAST / Resolution: 0.88→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 0 16 265 1254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.036
X-RAY DIFFRACTIONs_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.134
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0.106

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