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- PDB-4lqz: Crystal structure of a DUF4909 family protein (SAV1798) from Stap... -

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Basic information

Entry
Database: PDB / ID: 4lqz
TitleCrystal structure of a DUF4909 family protein (SAV1798) from Staphylococcus aureus subsp. aureus Mu50 at 1.92 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Streptavidin-like fold / PF16253 family / DUF4909 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Protein of unknown function DUF4909 / Protein of unknown function DUF4909 / Domain of unknown function (DUF4909) / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / DUF4909 domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (SAV1798) from Staphylococcus aureus subsp. aureus Mu50 at 1.92 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6393
Polymers17,5081
Non-polymers1302
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.352, 60.352, 37.388
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

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Components

#1: Protein Uncharacterized protein


Mass: 17508.178 Da / Num. of mol.: 1 / Fragment: UNP residues 34-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV1798 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q99T72, UniProt: A0A0H3JZY6*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (34-160) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 1.94 Å3/Da / Density % sol: 36.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 50.00% polyethylene glycol 200, 0.200M sodium chloride, 0.1M phosphate-citrate pH 4.2, 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: 0.97987,0.91837,0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 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
10.979871
20.918371
30.97931
ReflectionResolution: 1.92→42.675 Å / Num. obs: 10252 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.68 % / Biso Wilson estimate: 26.209 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.92-1.993.230.6511.72296291886.4
1.99-2.070.4012.83959104099.6
2.07-2.160.3193.7369096399.6
2.16-2.280.2784.24043108999.3
2.28-2.420.1925.93690100098.5
2.42-2.60.1667.13858101299.7
2.6-2.870.11110.13888107199.2
2.87-3.280.06217.93905102599.5
3.28-4.130.03529.23892105599.2
4.13-42.6750.02937.33872107997.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.92→42.675 Å / Cor.coef. Fo:Fc: 0.9498 / Cor.coef. Fo:Fc free: 0.9258 / Occupancy max: 1 / Occupancy min: 0.37 / 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 MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. PHOSPHATE (PO4) AND CHLORIDE (CL) IONS ARE PRESENT IN CRYSTALLIZATION CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 494 4.82 %RANDOM
Rwork0.1946 ---
obs0.1967 10255 97.88 %-
Displacement parametersBiso max: 122.45 Å2 / Biso mean: 44.5391 Å2 / Biso min: 18.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.8052 Å20 Å20 Å2
2--0.8052 Å20 Å2
3----1.6105 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 1.92→42.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 6 82 1148
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d511SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes29HARMONIC2
X-RAY DIFFRACTIONt_gen_planes163HARMONIC5
X-RAY DIFFRACTIONt_it1106HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion145SEMIHARMONIC5
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_contact1271SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1106HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1502HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion2.97
LS refinement shellResolution: 1.92→2.15 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2474 132 4.71 %
Rwork0.212 2668 -
all0.2137 2800 -
obs--97.88 %
Refinement TLS params.Method: refined / Origin x: 17.7342 Å / Origin y: 11.4801 Å / Origin z: 6.5624 Å
111213212223313233
T-0.2235 Å20.0188 Å2-0.015 Å2--0.2084 Å2-0.0458 Å2--0.113 Å2
L5.1706 °2-2.9104 °21.4095 °2-6.4684 °2-0.202 °2--1.5493 °2
S0.2341 Å °0.2902 Å °-0.5442 Å °-0.3971 Å °-0.182 Å °0.5442 Å °-0.0054 Å °0.1973 Å °-0.0521 Å °
Refinement TLS groupSelection details: { A|-6 - A|157 }

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