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- PDB-3ift: Crystal structure of glycine cleavage system protein H from Mycob... -

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Basic information

Entry
Database: PDB / ID: 3ift
TitleCrystal structure of glycine cleavage system protein H from Mycobacterium tuberculosis, using X-rays from the Compact Light Source.
ComponentsGlycine cleavage system H protein
KeywordsOXIDOREDUCTASE / NIAID / DECODE / UW / SBRI / GLYCINE CLEAVAGE SYSTEM / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / Seattle Structural Genomics Center for Infectious Disease / Lipoyl / methylamine binding protein
Function / homology
Function and homology information


glycine cleavage complex / glycine decarboxylation via glycine cleavage system / cytoplasm / cytosol
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 / Glycine cleavage system H protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEdwards, T.E. / Abendroth, J. / Staker, B. / Mayer, C. / Phan, I. / Kelley, A. / Analau, E. / Leibly, D. / Rifkin, J. / Loewen, R. ...Edwards, T.E. / Abendroth, J. / Staker, B. / Mayer, C. / Phan, I. / Kelley, A. / Analau, E. / Leibly, D. / Rifkin, J. / Loewen, R. / Ruth, R.D. / Stewart, L.J. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)
CitationJournal: J.Struct.Funct.Genom. / Year: 2010
Title: X-ray structure determination of the glycine cleavage system protein H of Mycobacterium tuberculosis using an inverse Compton synchrotron X-ray source.
Authors: Abendroth, J. / McCormick, M.S. / Edwards, T.E. / Staker, B. / Loewen, R. / Gifford, M. / Rifkin, J. / Mayer, C. / Guo, W. / Zhang, Y. / Myler, P. / Kelley, A. / Analau, E. / Hewitt, S.N. / ...Authors: Abendroth, J. / McCormick, M.S. / Edwards, T.E. / Staker, B. / Loewen, R. / Gifford, M. / Rifkin, J. / Mayer, C. / Guo, W. / Zhang, Y. / Myler, P. / Kelley, A. / Analau, E. / Hewitt, S.N. / Napuli, A.J. / Kuhn, P. / Ruth, R.D. / Stewart, L.J.
History
DepositionJul 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine cleavage system H protein


Theoretical massNumber of molelcules
Total (without water)15,2451
Polymers15,2451
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycine cleavage system H protein

A: Glycine cleavage system H protein


Theoretical massNumber of molelcules
Total (without water)30,4892
Polymers30,4892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1830 Å2
ΔGint-6 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.450, 51.010, 32.570
Angle α, β, γ (deg.)90.00, 95.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycine cleavage system H protein


Mass: 15244.579 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: GCHV, gcvH, MT1874, MTCY1A11.17c, Rv1826 / Plasmid: AVA0421 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q50607, UniProt: P9WN55*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.35 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 1.5M SODIUM CITRATE, 50MM BISTRIS PH 6.3; MYTUD.01046.A AT 27MG/ML, , VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.81836 / Wavelength: 0.81836 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81836 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 9535 / Num. obs: 9535 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 21.39 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.17
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 3.2 / Num. unique all: 710 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3hgb

3hgb


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.539 / SU ML: 0.129 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE riding position
RfactorNum. reflection% reflectionSelection details
Rfree0.253 459 4.8 %RANDOM
Rwork0.181 ---
obs0.185 9535 98.9 %-
all-9535 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.21 Å2
2--0.76 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms999 0 0 161 1160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211022
X-RAY DIFFRACTIONr_bond_other_d0.0010.02618
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9591405
X-RAY DIFFRACTIONr_angle_other_deg0.85831526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1825137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10325.58143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98815145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.186154
X-RAY DIFFRACTIONr_chiral_restr0.0760.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211175
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02191
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_it0.9191.5676
X-RAY DIFFRACTIONr_mcbond_other0.2111.5278
X-RAY DIFFRACTIONr_mcangle_it1.66821089
X-RAY DIFFRACTIONr_scbond_it2.3523346
X-RAY DIFFRACTIONr_scangle_it3.6774.5315
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 28 -
Rwork0.21 676 -
obs--99.44 %

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