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- PDB-4yjw: Crystal structure of a DUF3829 family protein (BVU_3067) from Bac... -

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Basic information

Entry
Database: PDB / ID: 4yjw
TitleCrystal structure of a DUF3829 family protein (BVU_3067) from Bacteroides vulgatus ATCC 8482 at 1.80 A resolution
ComponentsDUF3829 family protein
KeywordsSTRUCTURAL GENOMICS UNKNOWN FUNCTION / All alpha protein / PF12889 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / UNKNOWN FUNCTION
Function / homologyUncharacterised protein PF12889, N-terminal DUF3829 / : / Domain of unknown function (DUF6845) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha / DUF3829 domain-containing protein
Function and homology information
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a DUF3829 family protein (BVU_3067) from Bacteroides vulgatus ATCC 8482 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF3829 family protein


Theoretical massNumber of molelcules
Total (without water)19,5621
Polymers19,5621
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.766, 70.766, 67.473
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DUF3829 family protein


Mass: 19562.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (strain ATCC 8482 / DSM 1447 / NCTC 11154) (bacteria)
Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_3067 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6L4U0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 2.40M ammonium sulfate, 0.1M Bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2015
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→28.652 Å / Num. obs: 16483 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.17 % / Biso Wilson estimate: 21.665 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.088 / Net I/σ(I): 16.13 / Num. measured all: 187648
Reflection shell
Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
1.8-1.860.6510.7391.912263285928580.8431100
1.86-1.940.8170.6052.919008322332230.664100
1.94-2.030.9090.4274.419963311731170.465100
2.03-2.130.9610.2686.918244284328430.291100
2.13-2.270.9830.1821020532319431940.199100
2.27-2.440.9910.13912.819050295229520.151100
2.44-2.690.9940.10516.719929308530850.114100
2.69-3.070.9970.07422.619338299229920.08100
3.07-3.870.9990.04335.619617305730570.047100
3.87-28.6520.9990.0314719704308430730.03499.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XDSNovember 3, 2014 BUILT=20141118data scaling
BUSTER-TNT2.10.2refinement
XSCALEdata scaling
SHELXDphasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→28.652 Å / Cor.coef. Fo:Fc: 0.9532 / Cor.coef. Fo:Fc free: 0.9459 / 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. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. A UNMODELED DENSITY BLOB AT THE TWO-FOLD AXIS (NEAR A62) COULD BE EXPLAINED BY A BENZOIC ACID-LIKE COMPOUND.
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 832 5.06 %RANDOM
Rwork0.1732 ---
obs0.1743 16437 99.99 %-
Displacement parametersBiso max: 116.07 Å2 / Biso mean: 28.9582 Å2 / Biso min: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.2102 Å20 Å20 Å2
2---0.2102 Å20 Å2
3---0.4204 Å2
Refine analyzeLuzzati coordinate error obs: 0.202 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 0 184 1420
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d658SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes195HARMONIC5
X-RAY DIFFRACTIONt_it1325HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion174SEMIHARMONIC5
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_contact1726SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1325HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1809HARMONIC20.84
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion2.51
LS refinement shellResolution: 1.8→1.92 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2274 145 4.98 %
Rwork0.1972 2768 -
all0.1987 2913 -
obs--99.99 %
Refinement TLS params.Method: refined / Origin x: 22.4158 Å / Origin y: -2.5951 Å / Origin z: 17.8809 Å
111213212223313233
T-0.052 Å2-0.0055 Å2-0.0191 Å2--0.045 Å2-0.026 Å2---0.0273 Å2
L1.763 °2-1.886 °2-0.2327 °2-1.9631 °20.1342 °2--0.8344 °2
S-0.1163 Å °-0.133 Å °0.2104 Å °0.124 Å °0.1746 Å °-0.2959 Å °-0.1108 Å °-0.0296 Å °-0.0583 Å °
Refinement TLS groupSelection details: {A|34 - 186}

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