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- PDB-2q9r: CRYSTAL STRUCTURE OF a DUF416 family protein (SBAL_3149) FROM SHE... -

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Basic information

Entry
Database: PDB / ID: 2q9r
TitleCRYSTAL STRUCTURE OF a DUF416 family protein (SBAL_3149) FROM SHEWANELLA BALTICA OS155 AT 1.91 A RESOLUTION
ComponentsProtein of unknown function
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


YP_001051499.1 fold like / YP_001051499.1 domain like / Protein of unknown function DUF416 / YP001051499.1-like domain superfamily / Protein of unknown function (DUF416) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / BENZOIC ACID / DUF416 domain-containing protein
Similarity search - Component
Biological speciesShewanella baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function (YP_001051499.1) from Shewanella baltica OS155 at 1.91 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 24, 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 1.6Jan 25, 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 1.7Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY AND SURFACE ANALYSIS SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,35811
Polymers22,4321
Non-polymers92610
Water2,234124
1
A: Protein of unknown function
hetero molecules

A: Protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,71622
Polymers44,8642
Non-polymers1,85220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)68.570, 77.140, 87.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-202-

ACT

21A-202-

ACT

31A-263-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY AND PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein of unknown function


Mass: 22431.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella baltica (bacteria) / Strain: OS155 / Gene: YP_001051499.1, Sbal_3149 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3D7B7

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Non-polymers , 5 types, 134 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: NANODROP, 2.4M (NH4)2SO4, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97922, 0.97905
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 3, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979221
30.979051
ReflectionResolution: 1.91→29.062 Å / Num. obs: 18196 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.205 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 13.64
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.91-1.980.6331.682783432197.2
1.98-2.060.4742.285633456199.7
2.06-2.150.3273.281193329199.4
2.15-2.260.2424.581353320199.3
2.26-2.410.1616.291953665199.3
2.41-2.590.1158.683693337199.6
2.59-2.850.0812.186503462199.7
2.85-3.260.04719.287263459199.9
3.26-4.10.02733.386233453199.8
4.1-29.0620.0174586693444197.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.91→29.062 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.625 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.132
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE BENZOIC ACID (BEZ) MOLECULE IS ASSIGNED BASED ON THE ELECTRON DENSITY AND ITS INTERACTION WITH THE PROTEIN. IT COULD BE SOME RELATED COMPOUND WITH A SIMILAR STRUCTURE. 5. GOL, SO4 AND ACT ARE PRESENT IN CRYSTALLIZATION/CRYO BUFFER. ACT SITS ON SPECIAL POSITION AND COULD BE A NOISE.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 923 5.1 %RANDOM
Rwork0.169 ---
obs0.171 18169 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.634 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å20 Å2
2--1.07 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.91→29.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 59 124 1686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221610
X-RAY DIFFRACTIONr_bond_other_d0.0020.021040
X-RAY DIFFRACTIONr_angle_refined_deg1.4562.0082192
X-RAY DIFFRACTIONr_angle_other_deg0.97632577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.735206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0126.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33515266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.123154
X-RAY DIFFRACTIONr_chiral_restr0.0850.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021768
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02282
X-RAY DIFFRACTIONr_nbd_refined0.2210.2382
X-RAY DIFFRACTIONr_nbd_other0.1740.21001
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2809
X-RAY DIFFRACTIONr_nbtor_other0.0890.2779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.211
X-RAY DIFFRACTIONr_mcbond_it2.16931037
X-RAY DIFFRACTIONr_mcbond_other0.5473396
X-RAY DIFFRACTIONr_mcangle_it3.32551621
X-RAY DIFFRACTIONr_scbond_it5.9878646
X-RAY DIFFRACTIONr_scangle_it8.18611565
LS refinement shellResolution: 1.91→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 59 -
Rwork0.333 1213 -
obs-1272 97.47 %
Refinement TLS params.Method: refined / Origin x: 40.533 Å / Origin y: 22.086 Å / Origin z: -5.518 Å
111213212223313233
T-0.0469 Å20.0541 Å2-0.0033 Å2--0.0491 Å2-0.0518 Å2---0.0173 Å2
L0.5927 °20.4534 °20.4909 °2-1.269 °20.2252 °2--1.3045 °2
S0.0165 Å °-0.0737 Å °-0.0219 Å °-0.0338 Å °-0.0143 Å °0.05 Å °0.1229 Å °0.0715 Å °-0.0022 Å °

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