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- PDB-4egd: 1.85 Angstrom crystal structure of native hypothetical protein SA... -

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Basic information

Entry
Database: PDB / ID: 4egd
Title1.85 Angstrom crystal structure of native 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 / MOLECULAR REPLACEMENT / Resolution: 1.85 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: 1.85 Angstrom crystal structure of native 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 1.2Sep 13, 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 / database_2 / pdbx_initial_refinement_model / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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
B: Uncharacterized protein SAOUHSC_02783
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2124
Polymers61,1362
Non-polymers762
Water5,242291
1
A: Uncharacterized protein SAOUHSC_02783
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6082
Polymers30,5681
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein SAOUHSC_02783
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6032
Polymers30,5681
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.231, 88.782, 121.622
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: 30568.008 Da / Num. of mol.: 2 / 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 magic / References: UniProt: Q2FVD0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 1.95 Å3/Da / Density % sol: 37.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 7.3 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris, pH 8.3, screen: PACT, A3, 0.1 M SPG buffer, pH 6.0, 25% w/v PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.99984 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2011 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 41503 / Num. obs: 41503 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 24.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1842 / % possible all: 90.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EG9

4eg9


Resolution: 1.85→29.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.159 / SU ML: 0.057
Isotropic thermal model: THERMAL FACTORS INDIVIDUALLY REFINED
Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21527 2084 5 %RANDOM
Rwork0.1677 ---
all0.17017 39354 --
obs0.17017 39354 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---2 Å20 Å2
3---2.63 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3656 0 2 291 3949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0223846
X-RAY DIFFRACTIONr_bond_other_d0.0050.022735
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9665186
X-RAY DIFFRACTIONr_angle_other_deg0.96636687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3435461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07925.392204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64715732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9041518
X-RAY DIFFRACTIONr_chiral_restr0.1350.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02764
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_it2.2251.52273
X-RAY DIFFRACTIONr_mcbond_other0.8571.5910
X-RAY DIFFRACTIONr_mcangle_it3.33123709
X-RAY DIFFRACTIONr_scbond_it4.78131573
X-RAY DIFFRACTIONr_scangle_it7.0024.51477
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 151 -
Rwork0.224 2737 -
obs-2737 94.84 %
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)
11.01740.1105-0.03122.83240.71690.98030.01060.11350.134-0.0684-0.04770.3163-0.0199-0.0610.03710.07650.0247-0.01120.02960.00020.062722.482265.632514.6683
20.75260.0332-0.45284.5052-4.09347.30370.03240.03960.0689-0.14750.02710.05290.24160.0609-0.05950.02730.00780.0070.0425-0.03620.056633.717364.103526.0389
32.90820.95860.72872.15910.60961.64280.06470.12-0.0744-0.24710.0961-0.2088-0.14180.1901-0.16080.09110.01170.03520.0415-0.01860.028536.662163.994114.9956
43.4394-0.8665-0.65511.70.57290.728-0.00670.0442-0.0707-0.1857-0.03310.2027-0.0478-0.01760.03980.07470.0205-0.03230.0215-0.03010.065922.923551.807110.3918
53.6015-3.6941-0.52387.58350.80490.7288-0.17-0.1807-0.24010.49250.10040.47130.1423-0.03930.06960.1082-0.00240.00090.0392-0.02020.070424.969555.051818.776
61.3267-0.4804-0.02372.17020.49510.90270.0496-0.0035-0.1020.0257-0.03080.14730.0457-0.1177-0.01870.0045-0.0058-0.00360.01940.00410.017115.69659.572246.528
71.99760.9233-1.30923.3231-1.50094.63020.0663-0.0153-0.08240.09310.0233-0.1573-0.15330.0773-0.08950.01430.0171-0.01950.0636-0.03580.066531.51358.157640.8586
81.1364-0.6226-0.23651.82580.27131.2534-0.092-0.1247-0.06160.14130.06390.0479-0.03880.00780.02810.0535-0.0065-0.01410.0407-0.00640.039320.088667.447349.2148
93.7080.04270.74122.98750.34351.6509-0.11470.0510.16850.02210.0178-0.041-0.0458-0.01580.09690.04160.01410.00320.0304-0.00920.022618.564273.592551.2741
102.16471.04760.1096.37051.41241.28380.04580.08140.1896-0.4356-0.0266-0.0628-0.2106-0.0592-0.01920.05250.02310.01910.04310.01410.027919.4571.320444.1466
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 105
2X-RAY DIFFRACTION2A106 - 136
3X-RAY DIFFRACTION3A137 - 170
4X-RAY DIFFRACTION4A171 - 238
5X-RAY DIFFRACTION5A239 - 257
6X-RAY DIFFRACTION6B30 - 105
7X-RAY DIFFRACTION7B106 - 142
8X-RAY DIFFRACTION8B143 - 187
9X-RAY DIFFRACTION9B188 - 230
10X-RAY DIFFRACTION10B231 - 256

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