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- PDB-3k9i: Crystal structure of Putative protein binding protein (NP_241345.... -

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Basic information

Entry
Database: PDB / ID: 3k9i
TitleCrystal structure of Putative protein binding protein (NP_241345.1) from Bacillus halodurans at 2.71 A resolution
ComponentsBH0479 protein
KeywordsPROTEIN BINDING / Putative protein binding protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Tetratrico peptide repeat, group 5 / Tetratrico peptide repeat / Tetratricopeptide repeat domain / TPR repeat profile. / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.71 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative protein binding protein (NP_241345.1) from Bacillus halodurans at 2.71 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: 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

Downloads & links

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Assembly

Deposited unit
A: BH0479 protein


Theoretical massNumber of molelcules
Total (without water)13,1331
Polymers13,1331
Non-polymers00
Water00
1
A: BH0479 protein

A: BH0479 protein


Theoretical massNumber of molelcules
Total (without water)26,2662
Polymers26,2662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area3760 Å2
ΔGint-28 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.656, 73.656, 115.838
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein BH0479 protein / putative binding protein


Mass: 13132.761 Da / Num. of mol.: 1 / Fragment: sequence database reference 49-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: BH0479 / Plasmid: SpeedETS / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9KFK0
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 49-164) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 49-164) 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: 3.45 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.07
Details: 3.5M sodium formate, 0.1M HEPES pH 7.07, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97925,0.94926,0.97939
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.949261
30.979391
ReflectionResolution: 2.71→42.875 Å / Num. obs: 5493 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 85.26 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.03
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.71-2.810.7313.15349530199.3
2.81-2.920.5634.254935241100
2.92-3.050.3077.654725221100
3.05-3.210.19511.554365201100
3.21-3.410.1217.656065401100
3.41-3.670.08723.755995421100
3.67-4.040.0563555055441100
4.04-4.620.0424555435571100
4.62-5.80.04343.355185671100
5.8-42.8750.02850.75647645199.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.71→42.875 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 24.849 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.433 / ESU R Free: 0.263
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
Rfree0.233 245 4.5 %RANDOM
Rwork0.221 ---
obs0.221 5461 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.03 Å2 / Biso mean: 42.496 Å2 / Biso min: 16.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å20 Å2
2--0.68 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.71→42.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms874 0 0 0 874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022891
X-RAY DIFFRACTIONr_bond_other_d0.0010.02593
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9681205
X-RAY DIFFRACTIONr_angle_other_deg0.99631445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5475109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06824.65143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7215152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.762154
X-RAY DIFFRACTIONr_chiral_restr0.0870.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02186
X-RAY DIFFRACTIONr_mcbond_it1.5733543
X-RAY DIFFRACTIONr_mcbond_other0.3063225
X-RAY DIFFRACTIONr_mcangle_it2.8855861
X-RAY DIFFRACTIONr_scbond_it5.6938348
X-RAY DIFFRACTIONr_scangle_it8.17711344
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.472 13 -
Rwork0.315 363 -
all-376 -
obs--98.43 %
Refinement TLS params.Method: refined / Origin x: -5.4542 Å / Origin y: 47.5675 Å / Origin z: -0.0128 Å
111213212223313233
T0.3425 Å20.14 Å20.1315 Å2-0.2241 Å20.1029 Å2--0.2648 Å2
L1.8209 °20.673 °20.7118 °2-3.2456 °21.5726 °2--9.004 °2
S0.0492 Å °-0.0874 Å °-0.0162 Å °0.7635 Å °0.1048 Å °0.3783 Å °-0.4502 Å °-0.9648 Å °-0.1539 Å °

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