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- PDB-4mjf: Crystal structure of a DUF4348 family protein (BVU_2238) from Bac... -

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Basic information

Entry
Database: PDB / ID: 4mjf
TitleCrystal structure of a DUF4348 family protein (BVU_2238) from Bacteroides vulgatus ATCC 8482 at 1.99 A resolution
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF14254 family / DUF4348 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF4348 / Domain of unknown function (DUF4348) / Uncharacterized protein
Function and homology information
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BVU_2238) from Bacteroides vulgatus ATCC 8482 at 1.99 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 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: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,67216
Polymers31,3931
Non-polymers1,27915
Water2,216123
1
A: hypothetical protein
hetero molecules

A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,34432
Polymers62,7852
Non-polymers2,55830
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6540 Å2
ΔGint-178 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.719, 71.913, 65.504
Angle α, β, γ (deg.)90.000, 92.310, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-313-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein hypothetical protein


Mass: 31392.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_2238, YP_001299520.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6L2I4

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Non-polymers , 5 types, 138 molecules

#2: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT (25-286) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT (25-286) 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.200M lithium sulfate, 2.00M ammonium sulfate, 0.200M sodium thiocyanate, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97879
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 1.99→48.085 Å / Num. obs: 20233 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.225 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.044 / Net I/σ(I): 15.21 / Num. measured all: 67280
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.99-2.060.7280.5622.16720202019990.66999
2.06-2.140.8510.40836789199819760.48498.9
2.14-2.240.9240.2734.36989211720820.32698.3
2.24-2.360.9610.186.36599211220540.21797.3
2.36-2.510.9860.1139.87183209720710.13498.8
2.51-2.70.9930.07613.56617200919580.0997.5
2.7-2.970.9970.04919.16486205219770.05996.3
2.97-3.40.9990.03326.56853207220250.03997.7
3.4-4.270.9990.025336529206419920.02996.5
4.270.9980.0334.76515214620590.03695.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 1.99→48.085 Å / Cor.coef. Fo:Fc: 0.9586 / Cor.coef. Fo:Fc free: 0.9526 / Occupancy max: 1 / Occupancy min: 0.3 / 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. 3.ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.SULFATE (SO4), CAPS (CXS), CHLORIDE (CL) AND 1,2-ETHANEDIOL (EDO) FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTION HAVE BEEN MODELED. 5.RESIDUES 173-174 ARE IN A REGION OF ELECTRON DENSITY THAT IS NOT WELL-DEFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 1034 5.11 %RANDOM
Rwork0.1911 ---
obs0.1926 20230 97.81 %-
Displacement parametersBiso max: 145.03 Å2 / Biso mean: 55.0599 Å2 / Biso min: 31.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.1259 Å20 Å21.361 Å2
2--1.0088 Å20 Å2
3----1.1348 Å2
Refine analyzeLuzzati coordinate error obs: 0.317 Å
Refinement stepCycle: LAST / Resolution: 1.99→48.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 72 123 2087
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d944SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes286HARMONIC5
X-RAY DIFFRACTIONt_it2039HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion239SEMIHARMONIC5
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_contact2310SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2039HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2751HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion2.87
LS refinement shellResolution: 1.99→2.1 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2152 160 5.34 %
Rwork0.2089 2834 -
all0.2092 2994 -
obs--97.81 %
Refinement TLS params.Method: refined / Origin x: 28.0141 Å / Origin y: 64.2834 Å / Origin z: 17.8915 Å
111213212223313233
T-0.0698 Å20.1045 Å2-0.0019 Å2--0.0239 Å20.0753 Å2---0.0879 Å2
L0.645 °2-0.0621 °2-0.4588 °2-2.0787 °21.7487 °2--2.1713 °2
S-0.1326 Å °-0.0515 Å °-0.0237 Å °0.024 Å °0.099 Å °0.062 Å °0.1407 Å °0.1667 Å °0.0336 Å °
Refinement TLS groupSelection details: { A|60 - 286 }

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