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- PDB-4ebg: Crystal structure of a DUF4467 family protein (SAV0303) from Stap... -

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Basic information

Entry
Database: PDB / ID: 4ebg
TitleCrystal structure of a DUF4467 family protein (SAV0303) from Staphylococcus aureus subsp. aureus Mu50 at 1.35 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / secreted protein / PF14729 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Nuclear Transport Factor 2; Chain: A, - #560 / Domain of unknown function with cystatin-like fold DUF4467 / Domain of unknown function with cystatin-like fold (DUF4467) / Nuclear Transport Factor 2; Chain: A, / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DUF4467 domain-containing protein / DUF4467 domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (SAV0303) from Staphylococcus aureus subsp. aureus Mu50 at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5964
Polymers24,4392
Non-polymers1572
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-13 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.244, 35.058, 50.073
Angle α, β, γ (deg.)86.060, 79.660, 71.600
Int Tables number1
Space group name H-MP1
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 12219.255 Da / Num. of mol.: 2 / Fragment: UNP residues 25-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV0303 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q99WS4, UniProt: A0A0H3JX79*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 25-124 OF THE TARGET SEQUENCE.

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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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.20M ammonium dihydrogen phosphate, 20.00% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.2→17.689 Å / Num. all: 49882 / Num. obs: 49882 / % possible obs: 77.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.367 Å2 / Rsym value: 0.089 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.2-1.233.60.8850.71140932080.88567.4
1.23-1.263.60.7620.81316336470.76279.5
1.26-1.33.70.63911305535390.63978.1
1.3-1.343.60.5161.21164232320.51674.3
1.34-1.393.70.3981.61150730940.39873.4
1.39-1.433.70.3391.71246433260.33981.2
1.43-1.493.70.2741.21156031440.27479.9
1.49-1.553.70.1993.31049528720.19975.8
1.55-1.623.70.1674975826520.16771.9
1.62-1.73.70.1424.71063728600.14282.5
1.7-1.793.70.12651005427210.12682.3
1.79-1.93.70.1073.6929025180.10780.4
1.9-2.033.70.0897.2776820970.08971.4
2.03-2.193.80.087.7902623860.0886.8
2.19-2.43.80.0788.1794621120.07885.1
2.4-2.683.80.0768.1688618350.07679.2
2.68-3.13.80.0715.4557914780.07174.6
3.1-3.793.80.0639.3563115010.06388.5
3.79-5.373.70.0658.8375010010.06576.2
5.37-17.6893.80.0847.125146590.08491.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→17.689 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.442 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.047
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. PHOSPHATE (PO4) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 4. THE NOMINAL RESOLUTION IS 1.35 A WITH 14065 OBSERVED REFLECTIONS BETWEEN 1.35-1.20 (73.7% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.1673 2509 5 %RANDOM
Rwork0.1363 ---
obs0.1379 49737 77.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 56.94 Å2 / Biso mean: 19.6413 Å2 / Biso min: 7.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0.32 Å20.11 Å2
2--0.66 Å20.07 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.2→17.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 9 293 1938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221854
X-RAY DIFFRACTIONr_bond_other_d0.0010.021334
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9712511
X-RAY DIFFRACTIONr_angle_other_deg0.89933324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3125246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76126.436101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45915420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16156
X-RAY DIFFRACTIONr_chiral_restr0.1070.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022052
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02334
X-RAY DIFFRACTIONr_mcbond_it2.80631059
X-RAY DIFFRACTIONr_mcbond_other1.9243425
X-RAY DIFFRACTIONr_mcangle_it3.86851749
X-RAY DIFFRACTIONr_scbond_it58795
X-RAY DIFFRACTIONr_scangle_it7.22311735
X-RAY DIFFRACTIONr_rigid_bond_restr2.12533188
X-RAY DIFFRACTIONr_sphericity_free8.4313294
X-RAY DIFFRACTIONr_sphericity_bonded4.78533138
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 168 -
Rwork0.244 2965 -
all-3133 -
obs--66.21 %

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