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- PDB-5a4n: Crystal structure of BPSL1147, a PC4 homolog from Burkholderia ps... -

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Basic information

Entry
Database: PDB / ID: 5a4n
TitleCrystal structure of BPSL1147, a PC4 homolog from Burkholderia pseudomallei K96243 (tetragonal crystal form)
ComponentsBPSL1147
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / TRANSCRIPTION / DNA REPLICATION / RECOMBINATION AND REPAIR
Function / homologyTranscriptional coactivator p15 (PC4), C-terminal / Transcriptional Coactivator p15 (PC4) / ssDNA-binding transcriptional regulator / regulation of DNA-templated transcription / DNA binding / Transcriptional coactivator p15 (PC4) C-terminal domain-containing protein
Function and homology information
Biological speciesBURKHOLDERIA PSEUDOMALLEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsWerten, S. / Bayer, N. / Hinrichs, W.
CitationJournal: Gene / Year: 2016
Title: Structural Analysis and Knock-Out of a Burkholderia Pseudomallei Homolog of the Eukaryotic Transcription Coactivator Pc4.
Authors: Werten, S. / Kohler, C. / Bayer, N. / Steinmetz, I. / Hinrichs, W.
History
DepositionJun 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: BPSL1147
B: BPSL1147
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2536
Polymers17,1122
Non-polymers1424
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-63.4 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.527, 56.527, 142.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-2007-

HOH

21B-2025-

HOH

31B-2028-

HOH

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Components

#1: Protein BPSL1147


Mass: 8555.798 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: K96243 / Plasmid: PET-11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63VU8
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growTemperature: 295 K / pH: 8.5
Details: 20 MM TRIS/HCL PH 8.5, 2.1 M KCL, TEMPERATURE 295 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.96→47.5 Å / Num. obs: 17393 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.4
Reflection shellResolution: 1.96→2.08 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PCF, CHAINS A AND B WITH HELICAL REGIONS DELETED

1pcf


Resolution: 1.96→56.53 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.029 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25159 1712 9.8 %RANDOM
Rwork0.20984 ---
obs0.21373 15681 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.062 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.96→56.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 4 66 1162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191111
X-RAY DIFFRACTIONr_bond_other_d0.0010.021137
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9571500
X-RAY DIFFRACTIONr_angle_other_deg0.80532575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75620.18953
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91715204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9891521
X-RAY DIFFRACTIONr_chiral_restr0.0920.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021240
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02281
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8422.013544
X-RAY DIFFRACTIONr_mcbond_other1.8392.006543
X-RAY DIFFRACTIONr_mcangle_it3.022.99677
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3542.412567
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.957→2.008 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 123 -
Rwork0.323 1074 -
obs--95.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2519-0.3767-0.67012.3123-0.56062.98560.12180.44070.403-0.28910.14770.1454-0.0166-0.3395-0.26950.16880.04290.02450.12320.1250.149925.416414.676425.5646
27.38312.3454-5.6733.9391-4.47610.13720.2042-0.1542-0.05350.3181-0.2405-0.2427-0.08070.2570.03630.1775-0.0058-0.00890.0482-0.04130.147234.93418.016638.9515
30.8333-1.14490.29483.30351.40112.1116-0.0986-0.13070.3114-0.06880.1202-0.3921-0.2524-0.0257-0.02160.4098-0.07930.11080.0958-0.13330.335328.943919.59742.2822
46.223-1.7428-2.15826.02021.4654.77930.1323-0.07010.1315-0.10020.0273-0.07330.03870.0396-0.15960.1913-0.00360.00240.00590.00910.030327.42873.949933.4731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 57
2X-RAY DIFFRACTION2A58 - 73
3X-RAY DIFFRACTION3B6 - 57
4X-RAY DIFFRACTION4B58 - 73

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