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- PDB-3iwf: The Crystal Structure of the N-terminal domain of a RpiR Transcri... -

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Basic information

Entry
Database: PDB / ID: 3iwf
TitleThe Crystal Structure of the N-terminal domain of a RpiR Transcriptional Regulator from Staphylococcus epidermidis to 1.4A
ComponentsTranscription regulator RpiR family
Keywordstranscription regulator / RpiR / transcriptional / regulator / N-terminal / staphylococcus / epidermidis / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Helix-turn-helix protein RpiR / : / Helix-turn-helix domain, rpiR family / RpiR-type HTH domain profile. / RpiR-like, SIS domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Helix-turn-helix protein RpiR / : / Helix-turn-helix domain, rpiR family / RpiR-type HTH domain profile. / RpiR-like, SIS domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-METHOXYETHANOL / NICKEL (II) ION / Transcription regulator RpiR family / Transcription regulator RpiR family
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsStein, A.J. / Sather, A. / Borovilos, M. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of the N-terminal domain of a RpiR Transcriptional Regulator from Staphylococcus epidermidis to 1.4A
Authors: Stein, A.J. / Sather, A. / Borovilos, M. / Bargassa, M. / Joachimiak, A.
History
DepositionSep 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Transcription regulator RpiR family
B: Transcription regulator RpiR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,46811
Polymers24,8602
Non-polymers6089
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcription regulator RpiR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6996
Polymers12,4301
Non-polymers2695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Transcription regulator RpiR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7685
Polymers12,4301
Non-polymers3384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.921, 54.028, 173.044
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-163-

HOH

Detailsauthors state that biological unit is the same as asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transcription regulator RpiR family


Mass: 12429.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 12228 / Gene: SE1891, SE_1891 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8CNB1, UniProt: A0A0H2VHQ2*PLUS

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Non-polymers , 6 types, 177 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MXE / 2-METHOXYETHANOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG MME 2000, 0.1M Tris pH 8.5, 0.01M Nickel chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 45328 / % possible obs: 99.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.071 / Χ2: 2.563 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.454.40.61744941.02199.7
1.45-1.514.40.44444691.036199.8
1.51-1.584.40.30245241.061199.9
1.58-1.664.40.21145161.1311100
1.66-1.764.40.15244901.324199.9
1.76-1.94.40.11645321.6311100
1.9-2.094.40.08245472.274199.8
2.09-2.394.40.07345693.487199.9
2.39-3.024.30.06746435.3199.8
3.02-504.20.05445447.505194.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 1.4→30.7 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.18 / SU B: 1.842 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2287 5.1 %RANDOM
Rwork0.177 ---
obs0.179 45279 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.065 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 31 168 1647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221581
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.982148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3645197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.71524.84866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10915292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.183155
X-RAY DIFFRACTIONr_chiral_restr0.0830.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211149
X-RAY DIFFRACTIONr_mcbond_it1.331.5949
X-RAY DIFFRACTIONr_mcangle_it2.21321568
X-RAY DIFFRACTIONr_scbond_it3.2733632
X-RAY DIFFRACTIONr_scangle_it5.0344.5573
X-RAY DIFFRACTIONr_rigid_bond_restr1.42931581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.4360.3491620.33074329898.12
1.436-1.4760.2861620.2563068323699.815
1.476-1.5180.231400.2013032317899.811
1.518-1.5650.2261580.192893305299.967
1.565-1.6160.2111590.1682790295099.966
1.616-1.6730.1851510.1552767291999.966
1.673-1.7360.1891390.1412680282199.929
1.736-1.8060.1921480.1552510266299.85
1.806-1.8860.1851180.13424302548100
1.886-1.9780.161170.1442351247199.879
1.978-2.0850.1951140.162236235599.788
2.085-2.210.191190.1572106222699.955
2.21-2.3620.1771010.1642012211799.811
2.362-2.550.232970.1631860196099.847
2.55-2.7920.191950.181745184399.837
2.792-3.1180.207990.1851527163199.693
3.118-3.5940.211740.191406148499.73
3.594-4.3870.171700.1711158125198.161
4.387-6.1420.187450.208919101694.882
6.142-30.7010.439190.24842860474.007

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