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- PDB-4y1e: SAV1875-C105D -

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Basic information

Entry
Database: PDB / ID: 4y1e
TitleSAV1875-C105D
ComponentsUncharacterized protein SAV1875
KeywordsHYDROLASE / 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 / molecular replacement / Resolution: 1.8 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 1.1Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)39,4722
Polymers39,4722
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-3 kcal/mol
Surface area13520 Å2
Unit cell
Length a, b, c (Å)82.055, 93.946, 42.843
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: 19735.859 Da / Num. of mol.: 2 / Mutation: C105D
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 / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PPG400, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 31130 / % possible obs: 99 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.024 / Rrim(I) all: 0.088 / Χ2: 3.452 / Net I/av σ(I): 66.941 / Net I/σ(I): 14.9 / Num. measured all: 422814
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8313.90.39515100.9660.1090.412.46898.2
1.83-1.8613.60.35815440.9740.0990.3712.58498
1.86-1.913.90.3214870.980.0880.3322.68798.7
1.9-1.9413.60.27315450.9860.0760.2842.90298.7
1.94-1.9813.60.23615120.9860.0660.2453.14198.6
1.98-2.0313.50.20915240.9910.0580.2173.26198.7
2.03-2.0813.50.19215350.990.0540.1993.39698.8
2.08-2.1313.30.17315450.9920.0490.183.51798.8
2.13-2.213.40.15215410.9940.0430.1583.67799.1
2.2-2.2713.10.14215340.9930.0410.1483.67998.7
2.27-2.3513.40.13415450.9950.0380.1393.81498.8
2.35-2.4413.40.12115430.9950.0340.1263.89199.5
2.44-2.5513.40.11315610.9960.0320.1173.90399.6
2.55-2.6913.50.10215720.9970.0290.1064.11899.4
2.69-2.8613.70.09415640.9970.0260.0983.99299.6
2.86-3.0813.90.08615720.9970.0240.0894.11699.7
3.08-3.3913.90.07415800.9980.020.0774.13999.9
3.39-3.88140.06616130.9980.0180.0684.01199.8
3.88-4.8813.90.05616220.9980.0150.0583.42399.8
4.88-4013.10.04516810.9990.0130.0472.24897.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAV1875

Resolution: 1.8→31.65 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.213 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21765 1574 5.1 %RANDOM
Rwork0.18463 ---
obs0.18627 29520 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.088 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 0 136 2764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022694
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9593668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.28625.789133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.915447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1411512
X-RAY DIFFRACTIONr_chiral_restr0.150.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0212066
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: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 107 -
Rwork0.226 1867 -
obs--92.42 %
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)
10.5698-0.2486-0.00030.6372-0.25690.128-0.02080.00770.03240.04120.03430.003-0.0119-0.0057-0.01360.06410.0098-0.01020.0625-0.00110.05444.721-18.038-19.155
20.3425-0.44070.04220.7522-0.12650.3429-0.1288-0.0333-0.01160.10950.1106-0.0342-0.0136-0.03440.01820.10510.0227-0.00020.0734-0.00790.047318.201-40.661-5.679
30.3174-0.40320.12970.5843-0.16040.1994-0.07-0.0155-0.00770.06590.07430.0091-0.006-0.0126-0.00430.06560.0069-0.01240.06250.01030.05710.44-29.741-14.618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 172
2X-RAY DIFFRACTION2B2 - 172
3X-RAY DIFFRACTION3A201 - 270
4X-RAY DIFFRACTION3B201 - 266

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