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- PDB-5fbm: Crystal Structure of Histone Like Protein (HLP) from Streptococcu... -

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Basic information

Entry
Database: PDB / ID: 5fbm
TitleCrystal Structure of Histone Like Protein (HLP) from Streptococcus mutans Refined to 1.9 A Resolution
ComponentsDNA-binding protein HU
KeywordsDNA BINDING PROTEIN / Histone-like protein / DNA binding / Dimerization
Function / homology
Function and homology information


chromosome condensation / : / DNA binding
Similarity search - Function
HU Protein; Chain A / IHF-like DNA-binding proteins / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA-binding protein HU
Similarity search - Component
Biological speciesStreptococcus mutans serotype c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLovell, S. / Battaile, K.P. / Mehzabeen, N. / O'Neil, P. / Biswas, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE021664 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystal structure of histone-like protein from Streptococcus mutans refined to 1.9 angstrom resolution.
Authors: O'Neil, P. / Lovell, S. / Mehzabeen, N. / Battaile, K. / Biswas, I.
History
DepositionDec 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_audit_support / pdbx_struct_oper_list
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein HU
B: DNA-binding protein HU


Theoretical massNumber of molelcules
Total (without water)21,6592
Polymers21,6592
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-37 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.458, 76.333, 36.933
Angle α, β, γ (deg.)90.000, 107.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA-binding protein HU


Mass: 10829.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal hexahistidine tag
Source: (gene. exp.) Streptococcus mutans serotype c (strain ATCC 700610 / UA159) (bacteria)
Strain: ATCC 700610 / UA159 / Gene: hup, hlpA, SMU_589 / Plasmid: pIB-B39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9XB21
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.02 Å3/Da / Density % sol: 39.25 % / Description: Prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5 / Details: 30% PEG 400 and 0.1M CAPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→38.17 Å / Num. obs: 13437 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.033 / Net I/σ(I): 13.8 / Num. measured all: 45407 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.9-1.943.40.7141.929718820.710.45499.4
9.11-38.173.30.02640.13911190.9980.01787

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.04 Å38.17 Å
Translation3.04 Å38.17 Å

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Processing

Software
NameVersionClassification
Aimless0.2.14data scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RHI

3rhi


Resolution: 1.9→38.166 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 664 4.95 %
Rwork0.1766 12752 -
obs0.1785 13416 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.74 Å2 / Biso mean: 41.2287 Å2 / Biso min: 16.9 Å2
Refinement stepCycle: final / Resolution: 1.9→38.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1189 0 0 60 1249
Biso mean---43.81 -
Num. residues----166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011197
X-RAY DIFFRACTIONf_angle_d0.9621606
X-RAY DIFFRACTIONf_chiral_restr0.052196
X-RAY DIFFRACTIONf_plane_restr0.006203
X-RAY DIFFRACTIONf_dihedral_angle_d15.941424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-2.04680.30391450.24032549269499
2.0468-2.25270.23121390.18422537267699
2.2527-2.57860.21141220.168625872709100
2.5786-3.24860.23351350.18742574270999
3.2486-38.17420.19161230.16262505262896
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)
10.5766-0.00450.44620.1247-0.10290.34460.1025-0.6355-0.25030.12140.13020.16750.0355-0.75510.01510.26630.00680.01860.38120.02450.2488-0.357117.722316.9672
20.5641-0.36910.4450.2328-0.34110.3911-0.1386-0.02540.09420.068-0.0696-0.0728-0.07480.7885-0.00240.2658-0.0170.00540.25580.03430.22339.393721.91295.9109
30.43550.5946-0.56481.1626-0.72940.7973-0.0388-0.13560.2488-0.2182-0.63670.0876-0.2376-0.0554-0.92850.4160.2576-0.1220.29-0.12980.32842.427227.9122-14.5987
40.2614-0.1899-0.29120.11890.17680.3089-0.36580.4567-0.0017-0.03940.32290.42670.1611-0.4476-0.02930.2996-0.0099-0.00880.2452-0.01180.32271.037513.9705-4.83
50.425-0.70220.54391.2758-0.95570.72420.14290.13140.4616-0.1496-0.4804-0.14360.010.8577-0.11760.2073-0.0628-0.03020.361-0.00190.399915.666719.456110.9657
60.0566-0.0225-0.116400.02710.22230.00850.1706-0.20760.0667-0.0059-0.01240.13980.257200.2088-0.01310.00110.22730.02170.23294.739113.475510.505
70.31610.0785-0.29570.0739-0.06590.2760.33940.2396-0.17490.29320.04220.1541-0.051-0.7590.01850.2605-0.0165-0.02250.3446-0.02150.2862-5.28921.23455.2939
80.36190.42450.03090.55890.04240.01340.4182-0.26580.0305-0.2039-0.46770.1840.1177-0.440.02580.28950.0448-0.08040.3712-0.02640.2526-6.886717.001-3.5255
90.0360.0084-0.00920.0259-0.01850.01560.17450.01-0.326-0.13110.17960.2907-0.09630.05910.00260.3923-0.0864-0.07080.2307-0.01940.371-14.2913.7874-16.9716
100.0970.0457-0.0380.046-0.120.5673-0.02260.37090.0055-0.48670.23-0.3531-0.2466-0.30060.12130.33890.01860.06560.15530.01330.26110.060825.4968-3.6111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 18 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 48 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 74 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 92 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 18 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 38 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 39 through 48 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 56 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 57 through 74 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 75 through 91 )B0

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