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- PDB-5hbp: The crystal of rhodanese domain of YgaP treated with SNOC -

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Basic information

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


thiosulfate 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionJan 1, 2016Deposition 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 / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 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)14,0761
Polymers14,0761
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 area5570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.872, 43.872, 52.640
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.: 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: 2.08 Å3/Da / Density % sol: 40.93 %
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: May 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.5→38 Å / Num. obs: 16889 / % possible obs: 93.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / % possible all: 61.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HBL

5hbl


Resolution: 1.5→37.99 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.318 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18474 842 5 %RANDOM
Rwork0.17174 ---
obs0.17244 15970 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.367 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.5→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 3 147 937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019875
X-RAY DIFFRACTIONr_bond_other_d0.0020.02865
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.9771200
X-RAY DIFFRACTIONr_angle_other_deg0.9513.0022008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0465123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54325.34943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97915159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.893156
X-RAY DIFFRACTIONr_chiral_restr0.0780.2137
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_it0.8861.428434
X-RAY DIFFRACTIONr_mcbond_other0.8791.423432
X-RAY DIFFRACTIONr_mcangle_it1.4972.132544
X-RAY DIFFRACTIONr_mcangle_other1.4962.135545
X-RAY DIFFRACTIONr_scbond_it1.3021.611441
X-RAY DIFFRACTIONr_scbond_other1.31.612442
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1152.346646
X-RAY DIFFRACTIONr_long_range_B_refined5.23413.1491104
X-RAY DIFFRACTIONr_long_range_B_other4.88212.0841028
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.504→1.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 38 -
Rwork0.27 734 -
obs--57.91 %

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