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- PDB-4fc8: Crystal structure of transcription regulator protein Rtr1 from Kl... -

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Basic information

Entry
Database: PDB / ID: 4fc8
TitleCrystal structure of transcription regulator protein Rtr1 from Kluyveromyces lactis
Componentstranscription protein Rtr1
KeywordsTRANSCRIPTION / zinc finger
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat phosphatase activity / RNA polymerase core enzyme binding / myosin phosphatase activity / protein-serine/threonine phosphatase / metal ion binding / nucleus
Similarity search - Function
Rtr1/RPAP2 domain / Rtr1/RPAP2 domain / Rtr1/RPAP2 domain superfamily / Rtr1/RPAP2 / Rtr1/RPAP2 family / RTR1-type zinc finger. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase II subunit B1 CTD phosphatase RPAP2 homolog
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsXiang, K. / Tong, L.
CitationJournal: Nat Commun / Year: 2012
Title: The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity.
Authors: Xiang, K. / Manley, J.L. / Tong, L.
History
DepositionMay 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Data collection
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_asym_id / _struct_conn.ptnr2_label_asym_id / _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: transcription protein Rtr1
B: transcription protein Rtr1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6914
Polymers51,5612
Non-polymers1312
Water57632
1
A: transcription protein Rtr1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8462
Polymers25,7801
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: transcription protein Rtr1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8462
Polymers25,7801
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.168, 88.734, 94.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTwo molecules in one asymmetric unit

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Components

#1: Protein transcription protein Rtr1 /


Mass: 25780.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0F12672g, KLLA0_F12672g / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR / References: UniProt: Q6CK86
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THE FOLLOWING: THE FULL-LENGTH PROTEIN WAS DEGRADED DURING CRYSTALLIZATION, CONFIRMED ...AUTHORS STATE THE FOLLOWING: THE FULL-LENGTH PROTEIN WAS DEGRADED DURING CRYSTALLIZATION, CONFIRMED BY DISSOLVING THE CRYSTAL AND RUNNING IT ON AN SDS GEL. THE FRAGMENT THAT IS IN THE CRYSTAL MAY CONTAIN RESIDUES 1 to ~160. THIS WILL AFFECT THE CALCULATED SOLVENT CONTENT

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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: 1.84 Å3/Da / Density % sol: 33.24 %
Crystal growTemperature: 293 K / pH: 9.5
Details: 0.1M CHES pH 9.5 20% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.2833, 1.2836, 1.2652
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28331
21.28361
31.26521
ReflectionResolution: 2.5→50 Å / Num. obs: 24945 / % possible obs: 99.1 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.59 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 21.041 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.272 677 5 %RANDOM
Rwork0.222 ---
obs0.225 12890 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2---0.67 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 2 32 2280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9733079
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0195268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53823.772114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.76415428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4971519
X-RAY DIFFRACTIONr_chiral_restr0.1110.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211693
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_it0.7251.51361
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39422216
X-RAY DIFFRACTIONr_scbond_it2.1963920
X-RAY DIFFRACTIONr_scangle_it3.624.5863
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.63 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.321 93 -
Rwork0.285 1824 -
obs--98.41 %
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)
13.24491.91051.84043.94311.70721.91660.16270.327-0.05620.2828-0.0109-0.4180.2010.0228-0.15180.10990.019-0.01790.09450.0060.092410.145837.240246.1189
23.1035-0.149-2.75940.4449-0.03334.11630.0416-0.20550.0247-0.14060.03430.0243-0.26670.1273-0.07590.1774-0.0695-0.03510.0820.05030.05532.623462.592861.1211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 152
2X-RAY DIFFRACTION2B1 - 152

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