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- PDB-5hbl: Native rhodanese domain of YgaP prepared with 1mM DDT is S-nitros... -

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Basic information

Entry
Database: PDB / ID: 5hbl
TitleNative rhodanese domain of YgaP prepared with 1mM DDT is S-nitrosylated
ComponentsInner membrane protein YgaP
KeywordsTRANSFERASE / S-nitrosylation / S-sulfhydration. rhodanese
Function / homology
Function and homology information


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
Inner membrane protein YgaP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.617 Å
AuthorsEichmann, C. / Tzitzilonis, C. / Nakamura, T. / Kwiatkowski, W. / Maslennikov, I. / Choe, S. / Lipton, S.A. / Riek, R.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein.
Authors: Eichmann, C. / Tzitzilonis, C. / Nakamura, T. / Kwiatkowski, W. / Maslennikov, I. / Choe, S. / Lipton, S.A. / Riek, R.
History
DepositionDec 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Sep 8, 2021Group: Database references / Refinement description / Category: database_2 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)14,0761
Polymers14,0761
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.960, 43.960, 52.329
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: 14075.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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.: 149 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.617→52.31 Å / Num. obs: 14075 / % possible obs: 97.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 34.4
Reflection shellResolution: 1.617→1.623 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.9 / % possible all: 70

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
autoPROCdata reduction
autoPROCdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.617→38.07 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.674 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23572 686 5.1 %RANDOM
Rwork0.20333 ---
obs0.205 12805 93.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.652 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 1.617→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms798 0 2 149 949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019857
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9661171
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4795116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76325.12839
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32915147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.44155
X-RAY DIFFRACTIONr_chiral_restr0.0970.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021655
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0411.524438
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.742.273550
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5751.717419
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.98814.641470
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.617→1.659 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.699 37 -
Rwork0.287 800 -
obs--78.74 %

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