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- PDB-3sot: Crystal structure of a Multidomain protein including DUF1735 (BAC... -

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Basic information

Entry
Database: PDB / ID: 3sot
TitleCrystal structure of a Multidomain protein including DUF1735 (BACOVA_03322) from Bacteroides ovatus at 2.80 A resolution
ComponentsMultidomain protein including DUF1735
KeywordsStructural Genomics / Unknown Function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Uncharacterised protein PF14274, DUF4361 / Domain of unknown function DUF4361 / Domain of unknown function DUF4973 / BT_3044-like, C-terminal / Domain of unknown function (DUF4973) / hypothetical protein (bacova_03559) / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Immunoglobulin-like ...Uncharacterised protein PF14274, DUF4361 / Domain of unknown function DUF4361 / Domain of unknown function DUF4973 / BT_3044-like, C-terminal / Domain of unknown function (DUF4973) / hypothetical protein (bacova_03559) / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DUF4973 domain-containing protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, SAD / molecular replacement, SAD / Resolution: 2.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Multidomain protein including DUF1735 (BACOVA_03322) from Bacteroides ovatus at 2.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: 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: Multidomain protein including DUF1735
B: Multidomain protein including DUF1735
C: Multidomain protein including DUF1735
D: Multidomain protein including DUF1735
E: Multidomain protein including DUF1735
F: Multidomain protein including DUF1735
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,95510
Polymers224,7076
Non-polymers2484
Water2,468137
1
A: Multidomain protein including DUF1735
B: Multidomain protein including DUF1735
C: Multidomain protein including DUF1735
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6027
Polymers112,3533
Non-polymers2484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Multidomain protein including DUF1735
E: Multidomain protein including DUF1735
F: Multidomain protein including DUF1735


Theoretical massNumber of molelcules
Total (without water)112,3533
Polymers112,3533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.471, 123.339, 189.524
Angle α, β, γ (deg.)90.000, 99.280, 90.000
Int Tables number5
Space group name H-MC121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUGGESTS THAT A TRIMER IS A PREDOMINANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Multidomain protein including DUF1735


Mass: 37451.086 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_03322 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7LZP6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 22-339) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 22-339) 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: 2.32 Å3/Da / Density % sol: 47.03 %
Description: PHASER WAS USED FOR MOLECULAR REPLACEMENT USING 3NQK AS THE SEARCH MODEL. THE SELENIUM POSITIONS EXTRACTED FROM THIS MOLECULAR REPLACEMENT SOLUTION WERE USED FOR SAD PHASE REFINEMENT ...Description: PHASER WAS USED FOR MOLECULAR REPLACEMENT USING 3NQK AS THE SEARCH MODEL. THE SELENIUM POSITIONS EXTRACTED FROM THIS MOLECULAR REPLACEMENT SOLUTION WERE USED FOR SAD PHASE REFINEMENT WITHIN PHENIX.AUTOSOL. THE FINAL SAD PHASES WERE INCLDUED AS RESTRAINTS FOR REFINEMENT.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.2M MgAcetate, 20.00% PEG-3350, No Buffer, pH 7.7, 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
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2010
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 2.8→29.966 Å / Num. all: 49939 / Num. obs: 49939 / % possible obs: 98.9 % / Redundancy: 2.7 % / Rsym value: 0.161 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.8-2.872.60.6531.2961636750.65399.6
2.87-2.952.60.5581.4960736340.55899.5
2.95-3.042.60.4521.7926535150.45299.6
3.04-3.132.70.3642.1908334070.36499.4
3.13-3.232.70.3092.5886233120.30999.4
3.23-3.352.70.2572.9873432230.25799.3
3.35-3.472.70.1934840330980.19399.3
3.47-3.612.70.1754.3798129310.17599.1
3.61-3.782.70.1525772228430.15299.1
3.78-3.962.70.1335.7739826970.13398.9
3.96-4.172.70.1146.3700525690.11498.9
4.17-4.432.80.1026.9674424520.10298.7
4.43-4.732.70.0937.6629522980.09398.7
4.73-5.112.80.0977.1590321430.09798.2
5.11-5.62.70.1016.9530419380.10198.3
5.6-6.262.80.1156.2487817730.11598.1
6.26-7.232.70.1086.6427915570.10897.6
7.23-8.852.80.0917.4363813200.09197.4
8.85-12.522.70.0679.1282910330.06797.3
12.52-29.9662.70.069.114025210.0689.4

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Phasing

PhasingMethod: molecular replacement, SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
BUSTER-TNT2.8.0refinement
PHASERphasing
AutoSolphasing
SCALA3.3.15data scaling
MOSFLMdata reduction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SAD
Starting model: 3NQK

3nqk


Resolution: 2.8→29.966 Å / Cor.coef. Fo:Fc: 0.9005 / Cor.coef. Fo:Fc free: 0.8756 / 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. ETHYLENE GLYCOL USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE.4. THE REFINEMENT WAS RESTRAINBED AGAINST SAD PHASES. 5. NCS RESTRAINTS WERE APPLIED USING BUSTERS LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 2460 5.11 %RANDOM
Rwork0.2027 ---
obs0.2041 48168 --
Displacement parametersBiso max: 141.82 Å2 / Biso mean: 43.7968 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.5314 Å20 Å22.8658 Å2
2--3.2961 Å20 Å2
3----3.8275 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13691 0 16 137 13844
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6440SINUSOIDAL10
X-RAY DIFFRACTIONt_trig_c_planes395HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2010HARMONIC5
X-RAY DIFFRACTIONt_it14045HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1907SEMIHARMONIC5
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_contact15014SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14045HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg19087HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion1.87
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2834 170 5.1 %
Rwork0.2317 3166 -
all0.2343 3336 -
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)
12.5204-0.69860.76321.1-0.58151.87750.12730.3177-0.0813-0.1868-0.07260.09090.0748-0.0279-0.0547-0.15730.0011-0.0268-0.1283-0.012-0.09190.763330.5195-34.189
20.7424-0.1234-0.31381.57220.23491.18190.0418-0.06280.0034-0.0851-0.0367-0.20890.0856-0.0481-0.0051-0.08850.0433-0.0062-0.08590.0282-0.022932.972223.9508-14.6419
32.20430.5465-0.68611.5630.09751.334-0.0215-0.15890.088-0.1741-0.0006-0.1169-0.10660.13090.0221-0.11350.0321-0.0231-0.1436-0.0394-0.036122.34459.5662-21.7633
44.41111.67921.11341.47280.38722.2399-0.10590.5541-0.2491-0.04890.166-0.12440.0510.1451-0.0601-0.28750.0218-0.0098-0.1173-0.0867-0.230561.413829.1423-60.1565
53.7578-1.9120.45761.5918-0.43552.279-0.25210.73430.28430.3066-0.0745-0.0219-0.2397-0.01380.3266-0.184-0.1976-0.084-0.06220.0753-0.245237.715356.7116-71.0491
60.677-0.5937-0.49823.84050.55331.08020.20950.4009-0.24420.452-0.65960.57880.3836-0.18690.4501-0.2572-0.25690.03990.237-0.2483-0.27830.439623.5183-82.0736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|31 - 339 }A31 - 339
2X-RAY DIFFRACTION2{ B|32 - 339 }B32 - 339
3X-RAY DIFFRACTION3{ C|33 - 339 }C33 - 339
4X-RAY DIFFRACTION4{ D|31 - 339 }D31 - 339
5X-RAY DIFFRACTION5{ E|31 - 339 }E31 - 339
6X-RAY DIFFRACTION6{ F|41 - 339 }F41 - 339

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