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- PDB-4y1r: SAV1875-cysteinesulfonic acid -

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Basic information

Entry
Database: PDB / ID: 4y1r
TitleSAV1875-cysteinesulfonic acid
Components(Uncharacterized protein SAV1875) x 2
KeywordsHYDROLASE / DJ-1/PFPI/THIJ FAMILY
Function / homology
Function and homology information


Deglycase PfpI / PfpI endopeptidase domain profile. / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein SAV1875
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKim, H.J. / Kwon, A.R. / Lee, B.J.
CitationJournal: Biochem.J. / Year: 2016
Title: Structural and functional insight into the different oxidation states of SAV1875 from Staphylococcus aureus
Authors: Kim, H.J. / Kwon, A.R. / Lee, B.J.
History
DepositionFeb 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein SAV1875
B: Uncharacterized protein SAV1875


Theoretical massNumber of molelcules
Total (without water)39,5282
Polymers39,5282
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-1 kcal/mol
Surface area13470 Å2
Unit cell
Length a, b, c (Å)81.429, 94.715, 42.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uncharacterized protein SAV1875


Mass: 19771.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / Gene: SAV1875 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A0K0
#2: Protein Uncharacterized protein SAV1875


Mass: 19755.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / Gene: SAV1875 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A0K0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PPG400, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 39845 / % possible obs: 98.2 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.017 / Rrim(I) all: 0.059 / Χ2: 2.565 / Net I/av σ(I): 72.338 / Net I/σ(I): 23.5 / Num. measured all: 470168
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.687.60.23616570.9730.0890.2531.38683.1
1.68-1.718.10.22218040.9780.080.2371.47690.2
1.71-1.748.80.19418820.9860.0670.2061.60495.1
1.74-1.7810.50.1819660.9880.0570.191.64398.4
1.78-1.8212.20.15519920.9930.0450.1621.73999.9
1.82-1.8612.20.13620080.9950.040.1421.816100
1.86-1.912.20.12419810.9950.0370.131.941100
1.9-1.9612.30.10320370.9960.030.1082.117100
1.96-2.0112.50.08820110.9970.0260.0922.303100
2.01-2.0812.70.07919700.9980.0230.0832.47100
2.08-2.1512.80.07320370.9980.0210.0762.583100
2.15-2.24130.06520130.9990.0190.0682.639100
2.24-2.3413.20.06220050.9990.0180.0652.709100
2.34-2.4613.20.05920310.9990.0170.0612.829100
2.46-2.62130.05620430.9990.0160.0582.993100
2.62-2.8212.80.05320450.9990.0150.0553.125100
2.82-3.1112.50.05420290.9990.0160.0563.607100
3.11-3.5511.60.05120870.9990.0150.0544.08299.9
3.55-4.4811.70.04620760.9990.0140.0483.74599.9
4.48-4011.40.03721710.9980.0120.0392.8297.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y0N

4y0n


Resolution: 1.65→25.33 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.737 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21717 1993 5 %RANDOM
Rwork0.19012 ---
obs0.19147 37806 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.238 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.65→25.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 0 114 2727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022678
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9653648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.155344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54325.802131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51415442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7191512
X-RAY DIFFRACTIONr_chiral_restr0.3030.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0212048
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.647→1.689 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 111 -
Rwork0.21 2236 -
obs--83.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.49650.19830.0170.7343-0.18960.14050.0071-0.0224-0.0388-0.0390.0037-0.019-0.0052-0.0083-0.01080.0436-0.00390.00290.08190.00620.07634.62818.09718.737
20.8291.08180.05621.43680.0760.0196-0.25650.16020.0063-0.30390.2410.001-0.00770.00910.01550.1398-0.0579-0.00960.1348-0.00190.05417.50941.1195.713
30.63930.6258-0.10550.8472-0.23230.1089-0.0317-0.02970.0141-0.03890.02860.017-0.0255-0.01460.00310.0636-0.006700.0676-0.00480.07598.15729.13416.639
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 172
2X-RAY DIFFRACTION2B4 - 172
3X-RAY DIFFRACTION3A201 - 265
4X-RAY DIFFRACTION3B201 - 249

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