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- PDB-4y1f: SAV1875-E17D -

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Basic information

Entry
Database: PDB / ID: 4y1f
TitleSAV1875-E17D
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: 1.8 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 1.1Nov 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 1.2Oct 9, 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)39,4842
Polymers39,4842
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-3 kcal/mol
Surface area13590 Å2
Unit cell
Length a, b, c (Å)81.313, 94.150, 42.198
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: 19741.889 Da / Num. of mol.: 2 / Mutation: E17D
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.: 68 / 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: 2.05 Å3/Da / Density % sol: 39.87 %
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: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2014
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: 30762 / % possible obs: 99.3 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.03 / Rrim(I) all: 0.075 / Χ2: 4.153 / Net I/av σ(I): 58.176 / Net I/σ(I): 26.8 / Num. measured all: 221449
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.838.20.16315440.9880.0610.1742.891100
1.83-1.868.10.14814900.9890.0560.1593.008100
1.86-1.98.10.13715200.9910.0520.1473.091100
1.9-1.947.90.12515350.9920.0480.1343.322100
1.94-1.987.90.10815190.9940.0420.1163.581100
1.98-2.037.70.10215360.9940.040.1093.764100
2.03-2.087.70.09515210.9950.0370.1023.95499.9
2.08-2.137.60.0915280.9950.0360.0974.046100
2.13-2.27.50.08515270.9950.0340.0924.31399.9
2.2-2.277.50.07915320.9950.0320.0854.269100
2.27-2.357.40.07915560.9960.0310.0854.397100
2.35-2.447.30.07515140.9960.030.0814.469100
2.44-2.557.30.07315440.9950.0290.0794.607100
2.55-2.697.20.0715460.9950.0280.0754.725100
2.69-2.8670.06615510.9960.0270.0724.823100
2.86-3.086.70.06415490.9960.0270.0694.98899.9
3.08-3.396.10.06115570.9950.0270.0675.22999.7
3.39-3.885.70.05815840.9940.0280.0655.21399.6
3.88-4.885.50.05515610.9930.0270.0624.97697.9
4.88-405.80.05615480.9940.0260.0634.88890.4

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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: 1.8→29.31 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.45 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22444 1546 5 %RANDOM
Rwork0.19393 ---
obs0.19549 29169 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.534 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 0 68 2687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022661
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9663618
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9875339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69125.781128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55115439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5381512
X-RAY DIFFRACTIONr_chiral_restr0.1280.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0212026
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: 1.798→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 94 -
Rwork0.213 1961 -
obs--99.61 %
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)
10.69820.1921-0.02650.787-0.15890.1961-0.0033-0.0126-0.0212-0.04350.00360.00150.00320.0049-0.00040.0356-0.00780.00220.03570.0070.06384.45418.0618.747
20.62850.6632-0.05350.8463-0.00950.5851-0.16880.08310.0617-0.14830.1695-0.01360.0682-0.06-0.00070.085-0.0294-0.02370.0979-0.01810.083917.30141.2055.458
30.69980.496-0.18270.5704-0.14680.1091-0.0421-0.0062-0.0087-0.01220.01990.0213-0.030200.02220.0375-0.00830.0030.03890.0050.06858.81928.69116.095
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 172
2X-RAY DIFFRACTION2B3 - 172
3X-RAY DIFFRACTION3A201 - 240
4X-RAY DIFFRACTION3B201 - 228

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