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- PDB-5hpa: The crystal of rhodanese domain of YgaP treated with sodium thios... -

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Basic information

Entry
Database: PDB / ID: 5hpa
TitleThe crystal of rhodanese domain of YgaP treated with sodium thiosulfate
ComponentsInner membrane protein YgaP
KeywordsTRANSFERASE / S-sulfhydration. rhodanese
Function / homology
Function and homology information


thiosulfate sulfurtransferase / thiosulfate-cyanide sulfurtransferase activity / plasma membrane
Similarity search - Function
Inner membrane protein YgaP-like, transmembrane domain / Inner membrane protein YgaP-like, transmembrane domain / 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
Thiosulfate sulfurtransferase YgaP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsEichmann, C. / Tzitzilonis, C. / Kwiatkowski, W. / Riek, R.
CitationJournal: To Be Published
Title: S-Sulfhydration of the Catalytic Cysteine in the Rhodanese Domain of YgaP is a Complex Dynamical Process.
Authors: Eichmann, C. / Tzitzilonis, C. / Kwiatkowski, W. / Riek, R.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inner membrane protein YgaP


Theoretical massNumber of molelcules
Total (without water)14,0791
Polymers14,0791
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.699, 43.699, 52.280
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 Inner membrane protein YgaP


Mass: 14078.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ygaP, b2668, JW2643 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: P55734
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium acetate in 0.1 M Tris HCl pH 8.5, and 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.66→37.84 Å / Num. obs: 13126 / % possible obs: 98.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 34.4
Reflection shellResolution: 1.66→1.75 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.057 / Mean I/σ(I) obs: 16.2 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HBO

5hbo


Resolution: 1.66→37.84 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.564 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 645 4.9 %RANDOM
Rwork0.16708 ---
obs0.16845 12460 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.007 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.66→37.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms794 0 0 147 941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019873
X-RAY DIFFRACTIONr_bond_other_d0.0030.02863
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9741198
X-RAY DIFFRACTIONr_angle_other_deg0.9593.0012006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0765123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11825.34943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3515159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.197156
X-RAY DIFFRACTIONr_chiral_restr0.0760.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211009
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02185
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_it0.9451.412433
X-RAY DIFFRACTIONr_mcbond_other0.9391.409432
X-RAY DIFFRACTIONr_mcangle_it1.6312.11544
X-RAY DIFFRACTIONr_mcangle_other1.632.113545
X-RAY DIFFRACTIONr_scbond_it1.1941.571440
X-RAY DIFFRACTIONr_scbond_other1.1931.574441
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9142.292644
X-RAY DIFFRACTIONr_long_range_B_refined5.53712.7271097
X-RAY DIFFRACTIONr_long_range_B_other5.16911.751027
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.662→1.705 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 53 -
Rwork0.196 880 -
obs--96.38 %

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