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- PDB-3kny: Crystal structure of a two domain protein with unknown function (... -

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Basic information

Entry
Database: PDB / ID: 3kny
TitleCrystal structure of a two domain protein with unknown function (bt_3535) from bacteroides thetaiotaomicron vpi-5482 at 2.60 A resolution
Componentshypothetical protein BT_3535
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology: / BT_3535-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / Uncharacterized protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein BT_3535 (NP_812447.1) from BACTERIODES THETAIOTAOMICRON VPI-5482 at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 1.4Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 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
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein BT_3535


Theoretical massNumber of molelcules
Total (without water)24,6461
Polymers24,6461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein BT_3535

A: hypothetical protein BT_3535


Theoretical massNumber of molelcules
Total (without water)49,2922
Polymers49,2922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_764-x+2,-x+y+1,-z-1/31
Buried area1410 Å2
ΔGint0 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.029, 120.029, 94.767
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
DetailsANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein hypothetical protein BT_3535


Mass: 24645.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3535 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A1X3
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 18-234) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 18-234) 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: 4 Å3/Da / Density % sol: 69.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.93
Details: 40.9000% 2-methyl-2,4-pentanediol, 0.1M HEPES pH 6.93, 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: 0.91162,0.97941
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979411
ReflectionResolution: 2.6→28.831 Å / Num. obs: 12900 / % possible obs: 99.9 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 16.7
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.6710.70.7100299411.056100
2.67-2.7410.80.997019020.822100
2.74-2.8210.81.193998700.692100
2.82-2.9110.81.493698660.564100
2.91-310.71.890338420.44100
3-3.1110.82.485667900.326100
3.11-3.2210.7383997840.259100
3.22-3.3610.63.881207630.199100
3.36-3.5110.74.776307150.154100
3.51-3.6810.75.874637000.125100
3.68-3.8810.56.770876720.109100
3.88-4.1110.67.765806210.094100
4.11-4.3910.59.163326040.074100
4.39-4.7510.410.859025670.063100
4.75-5.210.410.853225130.061100
5.2-5.8110.39.649044780.07100
5.81-6.71109.242804290.073100
6.71-8.229.810.135763640.063100
8.22-11.639.310.928413040.053100
11.63-28.83812.413981750.04893.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→28.831 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.125 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.224
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 629 4.9 %RANDOM
Rwork0.202 ---
obs0.204 12878 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.95 Å2 / Biso mean: 39.252 Å2 / Biso min: 10.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20.64 Å20 Å2
2--1.28 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 0 0 1526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221573
X-RAY DIFFRACTIONr_bond_other_d0.0020.021068
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9592132
X-RAY DIFFRACTIONr_angle_other_deg0.81932620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7735194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51225.29468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35115274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.566154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02304
X-RAY DIFFRACTIONr_mcbond_it1.6753970
X-RAY DIFFRACTIONr_mcbond_other0.3133390
X-RAY DIFFRACTIONr_mcangle_it3.18751575
X-RAY DIFFRACTIONr_scbond_it5.1098603
X-RAY DIFFRACTIONr_scangle_it7.18411556
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 45 -
Rwork0.361 894 -
all-939 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 87.2446 Å / Origin y: 32.984 Å / Origin z: -4.0255 Å
111213212223313233
T0.1326 Å2-0.0389 Å20.0216 Å2-0.0877 Å20.0683 Å2--0.0905 Å2
L2.1646 °2-0.079 °20.0565 °2-2.1458 °2-0.502 °2--2.5958 °2
S0.0022 Å °-0.3427 Å °-0.4283 Å °0.3511 Å °-0.0696 Å °0.0818 Å °0.2689 Å °0.0283 Å °0.0674 Å °

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