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- PDB-1gmx: Escherichia coli GlpE sulfurtransferase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1gmx
TitleEscherichia coli GlpE sulfurtransferase
ComponentsTHIOSULFATE SULFURTRANSFERASE GLPE
KeywordsTRANSFERASE / RHODANESE / SULFURTRANSFERASE / GLYCEROL METABOLISM
Function / homology
Function and homology information


sulfur utilization / thiosulfate sulfurtransferase / glycerol metabolic process / thiosulfate-cyanide sulfurtransferase activity / cytoplasm
Similarity search - Function
Thiosulfate sulfurtransferase, bacterial / : / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Thiosulfate sulfurtransferase GlpE
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.1 Å
AuthorsSpallarossa, A. / Donahue, J.T. / Larson, T.J. / Bolognesi, M. / Bordo, D.
CitationJournal: Structure / Year: 2001
Title: Escherichia Coli Glpe is a Prototype Sulfurtransferase for the Single-Domain Rhodanese Homology Superfamily
Authors: Spallarossa, A. / Donahue, J.T. / Larson, T.J. / Bolognesi, M. / Bordo, D.
History
DepositionSep 25, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: THIOSULFATE SULFURTRANSFERASE GLPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,67710
Polymers12,1241
Non-polymers5539
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.870, 53.870, 30.523
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein THIOSULFATE SULFURTRANSFERASE GLPE / GLPE PROTEIN


Mass: 12124.485 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6V5, thiosulfate sulfurtransferase
#2: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 42 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
250 mMTris-HCl1droppH7.0
33 mMEDTA1drop
4100 mM1dropNaCl
510 %(v/v)glycerol1drop
60.1 M1reservoirCaCl2
70.1 Msodium acetate1reservoirpH4.6
820 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91
DetectorDate: Oct 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.06→20 Å / Num. obs: 45040 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 1.2 % / Rmerge(I) obs: 0.023 / Net I/σ(I): 43
Reflection shellResolution: 1.06→1.08 Å / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3 / % possible all: 93.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 555366
Reflection shell
*PLUS
% possible obs: 93.6 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.1→47 Å / SU B: 0.75 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R Free: 0.03
RfactorNum. reflection% reflectionSelection details
Rfree0.15112 2258 5 %RANDOM
Rwork0.12799 ---
obs0.12832 42521 99.6 %-
Refinement stepCycle: LAST / Resolution: 1.1→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 36 98 984
Refinement
*PLUS
Highest resolution: 1.06 Å / Lowest resolution: 47 Å / % reflection Rfree: 5 % / Rfactor obs: 0.128 / Rfactor Rfree: 0.151 / Rfactor Rwork: 0.128
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.3

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