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- PDB-3m7a: Crystal structure of Saro_0823 (YP_496102.1) a protein of unknown... -

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Basic information

Entry
Database: PDB / ID: 3m7a
TitleCrystal structure of Saro_0823 (YP_496102.1) a protein of unknown function from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.22 A resolution
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Uncharacterized ACR / COG1430
Function / homologyProtein of unknown function DUF192 / Protein of unknown function DUF192 / Saro_0823-like superfamily / Uncharacterized ACR, COG1430 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta / DUF192 domain-containing protein
Function and homology information
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.22 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of Saro_0823 (YP_496102.1) a protein of unknown function from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.22 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,6268
Polymers30,2532
Non-polymers3726
Water8,251458
1
A: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3134
Polymers15,1271
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3134
Polymers15,1271
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.401, 65.190, 59.730
Angle α, β, γ (deg.)90.000, 128.600, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

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Components

#1: Protein uncharacterized protein


Mass: 15126.579 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_0823 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2GA55
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 27-165) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THIS CONSTRUCT (RESIDUES 27-165) WAS EXPRESSED WITH AN N-TERMINAL 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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.86
Details: 29.5000% polyethylene glycol 4000, 0.2000M magnesium chloride, 0.1M TRIS pH 8.86, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97883,0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 2, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978831
20.918371
ReflectionResolution: 1.22→45.531 Å / Num. obs: 71683 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 8.037 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.24
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.22-1.260.6581.822928647397.2
1.26-1.310.5812.125656706297.5
1.31-1.370.4792.526277718697.9
1.37-1.450.3613.428955789098.1
1.45-1.540.274.728709703498.8
1.54-1.660.2067.138913718598.9
1.66-1.820.15910.647842687799.2
1.82-2.090.10116.855059742699.3
2.09-2.630.07822.653189718499.5
2.63-45.5310.05229.853509735399.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.22→45.531 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.216 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.037
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. ETHYLENE GLYCOL (EDO) MODELED WERE PRESENT IN CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.148 3565 5 %RANDOM
Rwork0.117 ---
obs0.119 71683 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.62 Å2 / Biso mean: 11.968 Å2 / Biso min: 3.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.2 Å2
2---0.39 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.22→45.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 24 458 2574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222342
X-RAY DIFFRACTIONr_bond_other_d0.0020.021648
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9893214
X-RAY DIFFRACTIONr_angle_other_deg0.89134043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.74422.82692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.68215390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3351523
X-RAY DIFFRACTIONr_chiral_restr0.0820.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02461
X-RAY DIFFRACTIONr_mcbond_it2.11531491
X-RAY DIFFRACTIONr_mcbond_other0.763594
X-RAY DIFFRACTIONr_mcangle_it2.92142438
X-RAY DIFFRACTIONr_scbond_it4.15851
X-RAY DIFFRACTIONr_scangle_it5.717754
X-RAY DIFFRACTIONr_rigid_bond_restr1.35133990
LS refinement shellResolution: 1.22→1.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 228 -
Rwork0.228 4925 -
all-5153 -
obs--96.99 %

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