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- PDB-4qdy: Crystal structure of a YbbR-like protein (SP_1560) from Streptoco... -

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Basic information

Entry
Database: PDB / ID: 4qdy
TitleCrystal structure of a YbbR-like protein (SP_1560) from Streptococcus pneumoniae TIGR4 at 2.74 A resolution
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two YbbR domains / PF07949 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyYbbR-like / : / YbbR-like protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / DI(HYDROXYETHYL)ETHER / Lipoprotein / Uncharacterized protein
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.74 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a conserved hypothetical protein (SP_1560) from Streptococcus pneumoniae TIGR4 at 2.74 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 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 1.5Oct 30, 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: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7454
Polymers24,4371
Non-polymers3083
Water21612
1
A: conserved hypothetical protein
hetero molecules

A: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4918
Polymers48,8742
Non-polymers6176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area3870 Å2
ΔGint-24 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.930, 77.930, 145.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein conserved hypothetical protein


Mass: 24436.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: NP_346007.1, SP_1560 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q97PP3, UniProt: A0A0H2UQV5*PLUS
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 34-259) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 34-259) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 42.0% polyethylene glycol 1500, 0.2M ammonium sulfate, 0.1M cesium chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97966,0.97895
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979661
30.978951
ReflectionResolution: 2.74→39.33 Å / Num. obs: 7389 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 69.717 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 18.36
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.74-2.842.79325727100
2.84-2.953.68626691100
2.95-3.084.6771669399.6
3.08-3.258999174599.6
3.25-3.4510.5936870499.7
3.45-3.71159286721100
3.71-4.0819.79023729100
4.08-4.6729.6846075399.9
4.67-5.8636.59576767100
5.8645.7917785898.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.74→39.33 Å / Cor.coef. Fo:Fc: 0.8878 / Cor.coef. Fo:Fc free: 0.8243 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE EXPERIMENTAL PHASES (MAD) WERE USED AS RESTRAINTS DURING REFINEMENT. 4. POLYETHYLENE GLYCOL FRAGMENTS (PEG) AND SULFATE FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.2878 342 4.64 %RANDOM
Rwork0.2323 ---
obs0.2346 7370 99.92 %-
Displacement parametersBiso max: 138.77 Å2 / Biso mean: 65.2071 Å2 / Biso min: 17.16 Å2
Baniso -1Baniso -2Baniso -3
1--13.3819 Å20 Å20 Å2
2---13.3819 Å20 Å2
3---26.7639 Å2
Refine analyzeLuzzati coordinate error obs: 0.482 Å
Refinement stepCycle: LAST / Resolution: 2.74→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 19 12 1479
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d685SINUSOIDAL10
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes211HARMONIC5
X-RAY DIFFRACTIONt_it1482HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion228SEMIHARMONIC10
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1658SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1482HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2026HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.06
X-RAY DIFFRACTIONt_other_torsion1.46
LS refinement shellResolution: 2.74→3.06 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.252 84 4.16 %
Rwork0.2695 1936 -
all0.2688 2020 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 36.5669 Å / Origin y: -2.8805 Å / Origin z: 44.4506 Å
111213212223313233
T0.07 Å20.2058 Å20.0271 Å2--0.1025 Å2-0.0217 Å2---0.0487 Å2
L0.4861 °20.2692 °20.1977 °2-1.7953 °2-0.8692 °2--1.2657 °2
S0.1081 Å °0.0928 Å °-0.071 Å °-0.0466 Å °-0.0986 Å °0.0079 Å °0.1905 Å °0.0517 Å °-0.0095 Å °
Refinement TLS groupSelection details: { A|33-230}

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