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- PDB-3tzu: Crystal structure of a glycine cleavage system H protein (GCVH) f... -

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Basic information

Entry
Database: PDB / ID: 3tzu
TitleCrystal structure of a glycine cleavage system H protein (GCVH) from Mycobacterium marinum
ComponentsGlycine cleavage system H protein 1
KeywordsTRANSPORT PROTEIN / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glycine cleavage complex / glycine decarboxylation via glycine cleavage system
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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Glycine cleavage system H protein
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Glycine cleavage system H protein 1
B: Glycine cleavage system H protein 1
C: Glycine cleavage system H protein 1
D: Glycine cleavage system H protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,39614
Polymers55,6934
Non-polymers70310
Water2,990166
1
A: Glycine cleavage system H protein 1
C: Glycine cleavage system H protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3669
Polymers27,8462
Non-polymers5207
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycine cleavage system H protein 1
D: Glycine cleavage system H protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0305
Polymers27,8462
Non-polymers1833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Glycine cleavage system H protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2756
Polymers13,9231
Non-polymers3515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Glycine cleavage system H protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1064
Polymers13,9231
Non-polymers1833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Glycine cleavage system H protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0913
Polymers13,9231
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Glycine cleavage system H protein 1


Theoretical massNumber of molelcules
Total (without water)13,9231
Polymers13,9231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.310, 50.310, 165.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Glycine cleavage system H protein 1 / / GCVH


Mass: 13923.193 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: gcvH_1, gcvH1, MMAR_0209 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2HKH2
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Internal tracking number 219005, JCSG screen D04: 0.1 M acetate, pH 4.5, 200 mM lithium sulfate, 30% w/v PEG8000, MymaA.01046.b.A1 PS00874 16.35 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2011
RadiationMonochromator: Si(220) asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.3→19.272 Å / Num. all: 20756 / Num. obs: 20740 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.151 % / Biso Wilson estimate: 38.42 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.64
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.265 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6624 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 3IFT

3ift


Resolution: 2.3→19.272 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.91 / SU B: 14.09 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.402 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1063 5.1 %RANDOM
Rwork0.184 ---
all0.187 20756 --
obs0.187 20740 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3590 0 46 166 3802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023719
X-RAY DIFFRACTIONr_bond_other_d0.0010.022273
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9725111
X-RAY DIFFRACTIONr_angle_other_deg0.9135642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6175510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05326.391133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32715478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.562158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02643
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 89 -
Rwork0.247 1465 -
obs-6624 99.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.31770.4338-0.98311.1968-0.55453.6809-0.0107-0.17170.21130.15920.09120.0333-0.4742-0.3949-0.08060.1190.13580.02220.17920.04210.1698-10.702119.9854-19.9425
23.4754-0.07430.74721.5589-0.69873.4802-0.10250.2191-0.1951-0.16420.17430.02650.4657-0.392-0.07180.1113-0.1312-0.01350.17260.02820.1376-10.66299.0413-49.0912
32.81640.13041.52970.99910.11834.0002-0.07220.1195-0.155-0.02080.06380.02750.39810.55350.00840.08770.11830.02610.20720.01660.108612.04224.0885-23.0925
42.5762-0.0178-1.9830.89410.25184.3093-0.0839-0.1160.1438-0.0120.06110.0448-0.38020.53410.02270.0937-0.1162-0.02540.20510.02420.11712.059724.9032-45.8177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 132
2X-RAY DIFFRACTION2B6 - 132
3X-RAY DIFFRACTION3C6 - 132
4X-RAY DIFFRACTION4D6 - 132

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