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- PDB-1xa8: Crystal Structure Analysis of Glutathione-dependent formaldehyde-... -

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Basic information

Entry
Database: PDB / ID: 1xa8
TitleCrystal Structure Analysis of Glutathione-dependent formaldehyde-activating enzyme (Gfa)
ComponentsGlutathione-dependent formaldehyde-activating enzyme
KeywordsLYASE / formaldehyde / glutathione / S-S bond
Function / homology
Function and homology information


S-(hydroxymethyl)glutathione synthase / S-(hydroxymethyl)glutathione synthase activity / formaldehyde catabolic process / zinc ion binding
Similarity search - Function
Glutathione-dependent formaldehyde-activating enzyme / glutathione-dependent formaldehyde- activating enzyme (gfa) / glutathione-dependent formaldehyde- activating enzyme (gfa) / CENP-V/GFA domain / Glutathione-dependent formaldehyde-activating enzyme / CENP-V/GFA domain profile. / Mss4-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutathione-dependent formaldehyde-activating enzyme
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNeculai, A.M. / Neculai, D. / Griesinger, C. / Vorholt, J.A. / Becker, S.
Citation
#1: Journal: J.Biol.Chem. / Year: 2002
Title: A glutathione-dependent formaldehyde-activating enzyme (Gfa) from Paracoccus denitrificans detected and purified via two-dimensional proton exchange NMR spectroscopy
Authors: Goenrich, M. / Bartoschek, S. / Hagemeier, C.H. / Griesinger, C. / Vorholt, J.A.
History
DepositionAug 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 21, 2012Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 25, 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_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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione-dependent formaldehyde-activating enzyme
B: Glutathione-dependent formaldehyde-activating enzyme
C: Glutathione-dependent formaldehyde-activating enzyme
D: Glutathione-dependent formaldehyde-activating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,01220
Polymers84,7644
Non-polymers2,24816
Water5,044280
1
A: Glutathione-dependent formaldehyde-activating enzyme
D: Glutathione-dependent formaldehyde-activating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,50810
Polymers42,3822
Non-polymers1,1268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-63 kcal/mol
Surface area18710 Å2
MethodPISA
2
B: Glutathione-dependent formaldehyde-activating enzyme
C: Glutathione-dependent formaldehyde-activating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,50410
Polymers42,3822
Non-polymers1,1228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-52 kcal/mol
Surface area18730 Å2
MethodPISA
3
A: Glutathione-dependent formaldehyde-activating enzyme
D: Glutathione-dependent formaldehyde-activating enzyme
hetero molecules

B: Glutathione-dependent formaldehyde-activating enzyme
C: Glutathione-dependent formaldehyde-activating enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,01220
Polymers84,7644
Non-polymers2,24816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area8740 Å2
ΔGint-129 kcal/mol
Surface area35900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.910, 120.620, 97.140
Angle α, β, γ (deg.)90.00, 97.68, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is a dimer

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glutathione-dependent formaldehyde-activating enzyme / Gfa


Mass: 21191.076 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: gfa / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q51669, Lyases; Carbon-sulfur lyases

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Non-polymers , 5 types, 296 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 3.6 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: (NH4)2SO4, HEPES, PEG400, 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 22, 2004 / Details: two Au coated X-ray mirrors
RadiationMonochromator: ROEMO type double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→96.27 Å / Num. all: 48095 / Num. obs: 48095 / % possible obs: 99.9 % / Observed criterion σ(F): 2.45 / Observed criterion σ(I): 2.09 / Redundancy: 1.96 % / Rmerge(I) obs: 0.0867 / Rsym value: 0.1104 / Net I/σ(I): 7.87
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 1.97 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.16 / Num. unique all: 5522 / Rsym value: 0.4849 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X6M

1x6m


Resolution: 2.4→75.16 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.482 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 2.09 / ESU R: 0.275 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24784 3425 7.1 %RANDOM
Rwork0.19507 ---
all0.19889 44668 --
obs0.19889 44668 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.344 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0.08 Å2
2---0.22 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.4→75.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 0 127 280 6311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0216200
X-RAY DIFFRACTIONr_angle_refined_deg2.0951.9668391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5435776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99822.982275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.87215966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3671555
X-RAY DIFFRACTIONr_chiral_restr0.1480.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024761
X-RAY DIFFRACTIONr_nbd_refined0.220.22339
X-RAY DIFFRACTIONr_nbtor_refined0.30.23903
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2313
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2840.210
X-RAY DIFFRACTIONr_mcbond_it0.9341.53997
X-RAY DIFFRACTIONr_mcangle_it1.62826227
X-RAY DIFFRACTIONr_scbond_it2.67732451
X-RAY DIFFRACTIONr_scangle_it3.9794.52164
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 258 -
Rwork0.262 3305 -
obs--100 %

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