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- PDB-4ifs: Crystal structure of the hSSRP1 Middle domain -

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Basic information

Entry
Database: PDB / ID: 4ifs
TitleCrystal structure of the hSSRP1 Middle domain
ComponentsFACT complex subunit SSRP1
KeywordsTRANSCRIPTION / REPLICATION / Double PH Domain / Histone / chaperone / Nucleus
Function / homology
Function and homology information


FACT complex / regulation of chromatin organization / nucleosome disassembly / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / nucleosome binding ...FACT complex / regulation of chromatin organization / nucleosome disassembly / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / nucleosome binding / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / nucleosome assembly / histone binding / Regulation of TP53 Activity through Phosphorylation / DNA replication / DNA repair / nucleolus / DNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
PH-domain like - #150 / : / FACT complex subunit SSRP1, C-terminal domain / : / SSRP1 PH domain / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / : ...PH-domain like - #150 / : / FACT complex subunit SSRP1, C-terminal domain / : / SSRP1 PH domain / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / : / Structure-specific recognition protein (SSRP1) / POB3-like N-terminal PH domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
FACT complex subunit SSRP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZhang, W.J. / Zeng, F.X. / Shao, C. / Liu, Y.W. / Niu, L.W. / Li, X. / Teng, M.K.
CitationJournal: To be Published
Title: Crystal structure of the hSSRP1 Middle domain
Authors: Zhang, W.J. / Zeng, F.X. / Shao, C. / Liu, Y.W. / Niu, L.W. / Li, X. / Teng, M.K.
History
DepositionDec 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: FACT complex subunit SSRP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5122
Polymers28,4771
Non-polymers351
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.187, 89.187, 82.589
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein FACT complex subunit SSRP1 / Chromatin-specific transcription elongation factor 80 kDa subunit / Facilitates chromatin ...Chromatin-specific transcription elongation factor 80 kDa subunit / Facilitates chromatin transcription complex 80 kDa subunit / FACT 80 kDa subunit / FACTp80 / Facilitates chromatin transcription complex subunit SSRP1 / Recombination signal sequence recognition protein 1 / Structure-specific recognition protein 1 / hSSRP1 / T160


Mass: 28476.807 Da / Num. of mol.: 1 / Fragment: MIDDLE DOMAIN, UNP RESIDUES 196-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FACT80, SSRP1 / Plasmid: slightly modified PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q08945
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG 6000, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 287.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.93→77.24 Å / Num. all: 29109 / Num. obs: 29080 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 26.618
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 4.857 / Num. unique all: 1441 / Rsym value: 0.496 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GCL

2gcl


Resolution: 1.93→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.731 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22053 1476 5.1 %RANDOM
Rwork0.19903 ---
all0.20024 27600 --
obs0.20008 27578 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 1 97 1981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221936
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.962612
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.675232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27922.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7615344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0491516
X-RAY DIFFRACTIONr_chiral_restr0.0750.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211459
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7881.51157
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46821880
X-RAY DIFFRACTIONr_scbond_it1.8413779
X-RAY DIFFRACTIONr_scangle_it3.0854.5732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.928→1.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 102 -
Rwork0.237 2019 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -35.2976 Å / Origin y: 22.7557 Å / Origin z: 35.1304 Å
111213212223313233
T0.1246 Å2-0.0349 Å20.0162 Å2-0.0676 Å20.026 Å2--0.0595 Å2
L3.6726 °22.2011 °2-0.1501 °2-1.6942 °2-0.0516 °2--0.7517 °2
S0.2488 Å °-0.0309 Å °0.1063 Å °0.2526 Å °-0.1205 Å °0.0925 Å °0.0839 Å °-0.0193 Å °-0.1283 Å °

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