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- PDB-2hdz: Crystal Structure Analysis of the UBF HMG box5 -

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Basic information

Entry
Database: PDB / ID: 2hdz
TitleCrystal Structure Analysis of the UBF HMG box5
ComponentsNucleolar transcription factor 1
KeywordsPROTEIN BINDING / HMG domain
Function / homology
Function and homology information


RNA polymerase I cis-regulatory region sequence-specific DNA binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase I Transcription Termination / positive regulation of transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape ...RNA polymerase I cis-regulatory region sequence-specific DNA binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase I Transcription Termination / positive regulation of transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / NoRC negatively regulates rRNA expression / fibrillar center / scaffold protein binding / chromatin binding / nucleolus / RNA binding / nucleoplasm / nucleus
Similarity search - Function
High mobility group box domain 5 / : / HMG (high mobility group) box 5 / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain ...High mobility group box domain 5 / : / HMG (high mobility group) box 5 / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleolar transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsRong, H. / Teng, M.K. / Niu, L.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of human upstream binding factor HMG box 5 and site for binding of the cell-cycle regulatory factor TAF1
Authors: Rong, H. / Li, Y. / Shi, X. / Zhang, X. / Gao, Y. / Dai, H. / Teng, M.K. / Niu, L.W. / Liu, Q. / Hao, Q.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleolar transcription factor 1


Theoretical massNumber of molelcules
Total (without water)10,8921
Polymers10,8921
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.812, 60.812, 63.158
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Nucleolar transcription factor 1 / Upstream-binding factor 1 / UBF-1 / Autoantigen NOR-90


Mass: 10891.573 Da / Num. of mol.: 1 / Fragment: HMG box 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBF / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17480
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews3/Da)Density % sol (%)
13.0960.25
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, hanging drop7.5NaCl, pH 7.5, vapor diffusion, hanging drop, temperature 277K
2772vapor diffusion, hanging drop7.5Se-Met derivate, pH 7.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.9363
SYNCHROTRONBSRF 3W1A20.97985
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDAug 24, 2004
MAR CCD 165 mm2CCDMay 3, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Bent triangular asymmetric cut Si(111) monochromaterSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.93631
20.979851
ReflectionResolution: 2→30 Å / Num. all: 9000 / Num. obs: 8917 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.046 / Rsym value: 0.049 / Χ2: 3.012 / Net I/σ(I): 35.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 10 % / Rmerge(I) obs: 0.185 / Num. unique all: 431 / Χ2: 2.468 / % possible all: 93.3

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 3 Å / D res low: 30 Å / FOM : 0.43 / Reflection: 2522
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.6470.6150.1671.867
2Se30.6590.6170.4360.0691.184
3Se56.2150.1910.6650.0581.283
4Se49.1670.7280.3840.0211.21
5Se46.0830.9930.5460.0151.338
Phasing MAD shell
Resolution (Å)FOM Reflection
10.49-300.54133
6.73-10.490.62217
5.29-6.730.56277
4.5-5.290.51324
3.98-4.50.39345
3.61-3.980.33382
3.32-3.610.37405
3.1-3.320.35439
Phasing dmFOM : 0.6 / FOM acentric: 0.6 / FOM centric: 0.49 / Reflection: 4494 / Reflection acentric: 4245 / Reflection centric: 249
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-27.1780.940.950.8719916930
4.5-7.10.890.910.6460955950
3.6-4.50.860.880.6574970940
3.1-3.60.720.730.5875571540
2.7-3.10.430.440.21353129360
2.5-2.70.220.220.0582980029

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.09phasing
RESOLVE2.09phasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCdata collection
RefinementMethod to determine structure: SAD / Resolution: 2→10 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.751 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 425 4.8 %RANDOM
Rwork0.217 ---
all0.22 8492 --
obs0.21953 8492 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.535 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å21.11 Å20 Å2
2--2.21 Å20 Å2
3----3.32 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms561 0 0 91 652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022571
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.961761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.993565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99124.48329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67715125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.373155
X-RAY DIFFRACTIONr_chiral_restr0.1020.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02418
X-RAY DIFFRACTIONr_nbd_refined0.20.2260
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.25
X-RAY DIFFRACTIONr_mcbond_it1.1141.5347
X-RAY DIFFRACTIONr_mcangle_it1.5042528
X-RAY DIFFRACTIONr_scbond_it3.0093271
X-RAY DIFFRACTIONr_scangle_it4.5394.5233
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 30 -
Rwork0.205 579 -
obs-609 95.6 %
Refinement TLS params.Method: refined / Origin x: 28.2352 Å / Origin y: -17.7616 Å / Origin z: 20.0748 Å
111213212223313233
T0.0077 Å2-0.0202 Å20.0036 Å2-0.0131 Å2-0.0005 Å2--0.029 Å2
L0.1835 °20.28 °2-0.4824 °2-1.0418 °20.0501 °2--2.2741 °2
S-0.0759 Å °0 Å °-0.0044 Å °0.04 Å °-0.0711 Å °-0.0895 Å °0.0108 Å °-0.2072 Å °0.1471 Å °

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