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- PDB-3s5t: Crystal structure of a member of duf3298 family (BF2082) from bac... -

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Basic information

Entry
Database: PDB / ID: 3s5t
TitleCrystal structure of a member of duf3298 family (BF2082) from bacteroides fragilis nctc 9343 at 2.30 A resolution
ComponentsDUF3298 family protein
KeywordsStructural Genomics / unknown function / PEPTIDOGLYCAN DEACETYLASE N-TERMINAL NONCATALYTIC REGION / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


Fervidobacterium nodosum Rt17-B1 like / Heat-shock cognate protein, ATPase / Deacetylase PdaC / Deacetylase PdaC / Domain of unknown function DUF3298 / PdaC/RsiV-like superfamily / Protein of unknown function (DUF3298) / Actin; Chain A, domain 4 / Heat Shock Protein 90 / Alpha-Beta Complex ...Fervidobacterium nodosum Rt17-B1 like / Heat-shock cognate protein, ATPase / Deacetylase PdaC / Deacetylase PdaC / Domain of unknown function DUF3298 / PdaC/RsiV-like superfamily / Protein of unknown function (DUF3298) / Actin; Chain A, domain 4 / Heat Shock Protein 90 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Member of DUF3298 family (BF2082) from Bacteroides fragilis NCTC 9343 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Nov 16, 2011Group: Structure summary
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.5Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF3298 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3207
Polymers30,7401
Non-polymers5806
Water99155
1
A: DUF3298 family protein
hetero molecules

A: DUF3298 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,63914
Polymers61,4802
Non-polymers1,16012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area5230 Å2
ΔGint-83 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.330, 98.330, 121.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein DUF3298 family protein


Mass: 30739.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF2082 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LDM9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 21-284) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 21-284) 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 10.0% 2-methyl-2,4-pentanediol, 0.2M lithium sulfate, 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: BL9-2 / Wavelength: 0.91837,0.97915,0.97892
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 20, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979151
30.978921
ReflectionResolution: 2.3→29.298 Å / Num. all: 15972 / Num. obs: 15972 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rsym value: 0.065 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.367.30.7311.1833311380.731100
2.36-2.427.30.6111.3822111270.611100
2.42-2.497.30.511.5795610920.51100
2.49-2.577.30.3762776610650.376100
2.57-2.667.20.332.3752510410.33100
2.66-2.757.30.2543734010110.254100
2.75-2.857.30.184468629450.184100
2.85-2.977.20.1285.868109410.128100
2.97-3.17.20.1126.664348930.112100
3.1-3.257.20.0867.763168730.086100
3.25-3.437.10.0758.458568210.075100
3.43-3.647.10.077.756327880.07100
3.64-3.897.10.0599.852667410.059100
3.89-4.27.10.04912.148626880.049100
4.2-4.670.04312.845166460.043100
4.6-5.146.90.03913.640995910.039100
5.14-5.946.80.04712.535495250.047100
5.94-7.276.40.05111.929594590.051100
7.27-10.296.20.0414.322973730.04100
10.29-29.2985.30.04213.311352140.04293.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
BUSTER-TNT2.8.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.298 Å / Cor.coef. Fo:Fc: 0.9571 / Cor.coef. Fo:Fc free: 0.9484 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0
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. MPD,CL, PO4 MODELED ARE PRESENT IN PROTEIN/CRYSTALLIZATION/ CRYO CONDITIONS. 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 794 4.98 %RANDOM
Rwork0.1863 ---
obs0.1874 15929 --
Displacement parametersBiso max: 184.47 Å2 / Biso mean: 69.052 Å2 / Biso min: 34.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.881 Å20 Å20 Å2
2---0.881 Å20 Å2
3---1.762 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 35 55 2117
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d966SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes306HARMONIC5
X-RAY DIFFRACTIONt_it2144HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion278SEMIHARMONIC5
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_contact2476SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2144HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2920HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion2.82
LS refinement shellResolution: 2.3→2.46 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2201 132 4.68 %
Rwork0.206 2690 -
all0.2067 2822 -
Refinement TLS params.Method: refined / Origin x: -14.4734 Å / Origin y: 77.2567 Å / Origin z: 7.4522 Å
111213212223313233
T-0.2316 Å20.0312 Å2-0.0173 Å2-0.0716 Å2-0.026 Å2---0.1524 Å2
L2.5648 °20.7705 °20.8604 °2-1.3425 °20.2924 °2--1.841 °2
S0.0621 Å °0.031 Å °-0.2061 Å °-0.0601 Å °0.1102 Å °-0.3203 Å °0.0725 Å °0.6375 Å °-0.1723 Å °
Refinement TLS groupSelection details: { A|28 - 284 }

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