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- PDB-4eg9: 1.9 Angstrom resolution crystal structure of Se-methionine hypoth... -

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Basic information

Entry
Database: PDB / ID: 4eg9
Title1.9 Angstrom resolution crystal structure of Se-methionine hypothetical protein SAOUHSC_02783 from Staphylococcus aureus
ComponentsUncharacterized protein SAOUHSC_02783
KeywordsUNKNOWN FUNCTION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyouter membrane lipoprotein receptor (LolB), chain A - #40 / Csa family / Csa superfamily / Csa1 family / outer membrane lipoprotein receptor (LolB), chain A / Clam / Mainly Beta / plasma membrane / Uncharacterized protein SAOUHSC_02783
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsBiancucci, M. / Minasov, G. / Halavaty, A. / Filippova, E.V. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. ...Biancucci, M. / Minasov, G. / Halavaty, A. / Filippova, E.V. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.9 Angstrom resolution crystal structure of Se-methionine hypothetical protein SAOUHSC_02783 from Staphylococcus aureus
Authors: Biancucci, M. / Minasov, G. / Halavaty, A. / Filippova, E.V. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center ...Authors: Biancucci, M. / Minasov, G. / Halavaty, A. / Filippova, E.V. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein SAOUHSC_02783
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9362
Polymers30,8961
Non-polymers401
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.346, 60.707, 94.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein SAOUHSC_02783


Mass: 30896.273 Da / Num. of mol.: 1 / Fragment: UNP residues 22-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: SAOUHSC_02783 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2FVD0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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 Å3/Da / Density % sol: 38.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 7.0 mg/mL protein in 0.25 M sodium chloride, 0.01 M Tris, pH 8.3, screen: TRAP, H1, 0.1 M HEPES, pH 7.0, 30% v/v Jeffamine, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 5, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 20233 / Num. obs: 19583 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1485 / % possible all: 80.3

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→28.89 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.746 / SU ML: 0.1
Isotropic thermal model: THERMAL FACTORS INDIVIDUALLY REFINED
Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27143 1007 5.1 %RANDOM
Rwork0.21533 ---
all0.21801 18575 --
obs0.21801 18575 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.798 Å2
Baniso -1Baniso -2Baniso -3
1--3.17 Å20 Å20 Å2
2---3.52 Å20 Å2
3---6.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 1 140 2050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222004
X-RAY DIFFRACTIONr_bond_other_d0.0010.021421
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.9642706
X-RAY DIFFRACTIONr_angle_other_deg0.79133470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6615242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89125.364110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56415376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7231511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212261
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02401
X-RAY DIFFRACTIONr_mcbond_it0.9771.51188
X-RAY DIFFRACTIONr_mcbond_other0.3141.5475
X-RAY DIFFRACTIONr_mcangle_it1.63221940
X-RAY DIFFRACTIONr_scbond_it2.8523816
X-RAY DIFFRACTIONr_scangle_it4.3094.5766
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 57 -
Rwork0.279 1156 -
obs-1156 83.25 %
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)
10.67911.4575-0.71795.5108-2.4141.82480.1808-0.02280.23970.30670.02950.363-0.151-0.1609-0.21030.16070.00740.03710.1499-0.00620.206814.971730.807851.702
21.74330.48190.38522.82571.29772.76910.0197-0.1975-0.09550.3124-0.11370.14410.04670.07070.09390.1758-0.00580.02430.19850.02210.01829.917331.211446.4521
31.20350.46090.47889.82535.68453.88290.17710.2032-0.01420.2088-0.0548-0.41470.29550.0249-0.12220.16170.02020.00120.22140.00710.147137.216523.683732.3509
41.75350.8155-0.64531.4514-0.68341.77890.00660.27490.2427-0.11770.10040.1406-0.0649-0.1163-0.1070.15970.0205-0.02270.1373-0.00440.187325.552535.246537.6615
51.635-0.14020.04392.3087-1.42563.96040.05380.1223-0.0214-0.0347-0.04520.08150.07570.0258-0.00860.10350.00940.0170.1402-0.0130.147616.251524.692742.0877
62.7322.82252.74044.2014.71328.57210.20310.0815-0.33570.36890.0342-0.050.42490.2169-0.23730.13810.03010.02390.1164-0.00820.158924.720823.108541.0027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 55
2X-RAY DIFFRACTION2A56 - 102
3X-RAY DIFFRACTION3A103 - 129
4X-RAY DIFFRACTION4A130 - 178
5X-RAY DIFFRACTION5A179 - 236
6X-RAY DIFFRACTION6A237 - 258

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