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- PDB-4y1g: SAV1875-E17N -

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Basic information

Entry
Database: PDB / ID: 4y1g
TitleSAV1875-E17N
ComponentsUncharacterized protein SAV1875
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: 1.9 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 7, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,4502
Polymers39,4502
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-2 kcal/mol
Surface area13820 Å2
Unit cell
Length a, b, c (Å)82.353, 95.647, 41.569
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: 19724.904 Da / Num. of mol.: 2 / Mutation: E17N
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PPG400, GnCl, 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: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 26532 / % possible obs: 99.8 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.03 / Rrim(I) all: 0.093 / Χ2: 3.202 / Net I/av σ(I): 55.051 / Net I/σ(I): 15.9 / Num. measured all: 251442
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9310.20.41812900.9650.1360.441.903100
1.93-1.9710.10.35113220.9740.1150.372.063100
1.97-2.0110.10.28913100.9780.0950.3042.2100
2.01-2.0510.20.26412960.9840.0860.2782.32100
2.05-2.0910.10.23613000.9850.0770.2492.43799.9
2.09-2.14100.19613080.9890.0650.2062.613100
2.14-2.19100.17213160.990.0570.1822.75999.8
2.19-2.25100.15612930.9920.0520.1652.89899.9
2.25-2.329.90.14513270.9920.0490.1542.925100
2.32-2.399.90.13412880.9930.0440.1413.068100
2.39-2.489.80.12113360.9950.0410.1283.269100
2.48-2.589.80.11213240.9950.0380.1193.384100
2.58-2.79.60.09813130.9960.0330.1043.629100
2.7-2.849.50.09113210.9950.0310.0963.771100
2.84-3.029.30.08513360.9960.0290.094.022100
3.02-3.258.80.07513410.9970.0270.084.346100
3.25-3.588.20.06813360.9960.0250.0734.691100
3.58-4.097.90.06313580.9970.0230.0674.76999.9
4.09-5.158.30.05913820.9980.0210.0624.49799.8
5.15-408.20.05214350.9960.0190.0563.56597.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y0N

4y0n


Resolution: 1.9→34.6 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.213 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21642 1339 5.1 %RANDOM
Rwork0.18754 ---
obs0.18901 25147 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 0 46 2702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022707
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9583681
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0095345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73125.714133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75915445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1351512
X-RAY DIFFRACTIONr_chiral_restr0.1030.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0212072
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: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 90 -
Rwork0.208 1651 -
obs--98.64 %
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)
11.29310.1769-0.0030.9961-0.35770.14210.00140.05960.11230.03850.06560.1273-0.007-0.0076-0.06690.04180.0151-0.00150.07110.02540.10464.321-19.138-17.948
20.2016-0.1985-0.17320.70560.07740.6526-0.05580.0232-0.04540.10320.0482-0.0355-0.0069-0.02240.00760.07540.0186-0.01510.0760.00330.054617.811-43.83-6.679
30.3564-0.36720.1950.7573-0.33180.153-0.02910.054-0.0150.06030.04220.0311-0.0315-0.0001-0.01310.07250.0071-0.01060.07890.02940.063313.418-33.625-13.864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 172
2X-RAY DIFFRACTION2B3 - 176
3X-RAY DIFFRACTION3A201 - 222
4X-RAY DIFFRACTION3B201 - 224

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