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- PDB-4flb: CID of human RPRD2 -

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Basic information

Entry
Database: PDB / ID: 4flb
TitleCID of human RPRD2
ComponentsRegulation of nuclear pre-mRNA domain-containing protein 2
KeywordsPROTEIN BINDING / structural genomics consortium / sgc
Function / homology
Function and homology information


RNA polymerase II, holoenzyme / snRNA transcription by RNA polymerase II / mRNA 3'-end processing / RNA polymerase II complex binding / RNA polymerase II transcribes snRNA genes / nucleoplasm
Similarity search - Function
Regulation of nuclear pre-mRNA domain-containing protein 1A/B / Cell-cycle alteration and expression-elevated protein in tumour / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
PRASEODYMIUM ION / Regulation of nuclear pre-mRNA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.802 Å
AuthorsNi, Z. / Xu, C. / Tempel, W. / El Bakkouri, M. / Loppnau, P. / Guo, X. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. ...Ni, Z. / Xu, C. / Tempel, W. / El Bakkouri, M. / Loppnau, P. / Guo, X. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Greenblatt, J.F. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation.
Authors: Ni, Z. / Xu, C. / Guo, X. / Hunter, G.O. / Kuznetsova, O.V. / Tempel, W. / Marcon, E. / Zhong, G. / Guo, H. / Kuo, W.H. / Li, J. / Young, P. / Olsen, J.B. / Wan, C. / Loppnau, P. / El ...Authors: Ni, Z. / Xu, C. / Guo, X. / Hunter, G.O. / Kuznetsova, O.V. / Tempel, W. / Marcon, E. / Zhong, G. / Guo, H. / Kuo, W.H. / Li, J. / Young, P. / Olsen, J.B. / Wan, C. / Loppnau, P. / El Bakkouri, M. / Senisterra, G.A. / He, H. / Huang, H. / Sidhu, S.S. / Emili, A. / Murphy, S. / Mosley, A.L. / Arrowsmith, C.H. / Min, J. / Greenblatt, J.F.
History
DepositionJun 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Structure summary
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Aug 20, 2014Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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: Regulation of nuclear pre-mRNA domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,23110
Polymers16,7571
Non-polymers4749
Water1,29772
1
A: Regulation of nuclear pre-mRNA domain-containing protein 2
hetero molecules

A: Regulation of nuclear pre-mRNA domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,46220
Polymers33,5142
Non-polymers94818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_466y-1,x+1,-z+11
Buried area3610 Å2
ΔGint-108 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.339, 40.339, 145.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT HAS NOT BEEN DETERMINED

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Components

#1: Protein Regulation of nuclear pre-mRNA domain-containing protein 2


Mass: 16757.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPRD2, KIAA0460, HSPC099 / Plasmid: pET15 MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 / References: UniProt: Q5VT52
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pr
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG-3350, 0.2M ammounium sulfate, 0.1M sodium cacodylate, praseodymium(III) acetate, pH 5.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→28.54 Å / Num. obs: 11740 / % possible obs: 98.86 % / Redundancy: 12.46 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 25.0113
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
1.8-1.912.730.75207321628197.08
1.9-2.0113.040.45204801570198.27
2.01-2.1513.090.24191311461198.63
2.15-2.3312.990.18180911393199.1
2.33-2.5512.840.14166621298199.31
2.55-2.8512.510.11149751197199.65
2.85-3.2912.310.07129521052199.74
3.29-4.0311.630.0510966943199.97
4.03-5.710.860.038083744199.96
5.7-28.529.340.034239454198.63

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
SHELXphasing
REFMAC5.7.0027refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.802→28.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.191 / WRfactor Rwork: 0.158 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.291 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. SAD PHASING WAS PERFORMED USING MERGED INTENSITIES FROM HKL3000 WITH THE "AUTO CORRECTIONS" OPTION FOR SCALEPACK. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. SAD PHASING WAS PERFORMED USING MERGED INTENSITIES FROM HKL3000 WITH THE "AUTO CORRECTIONS" OPTION FOR SCALEPACK. BUCCANEER AND ARP/WARP WERE USED FOR MODEL TRACING. COOT AND THE MOLPROBITY SERVER WERE ALSO USED DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 552 4.714 %RANDOM
Rwork0.1746 ---
obs0.177 11711 98.387 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 54.08 Å2 / Biso mean: 20.391 Å2 / Biso min: 9.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.149 Å20 Å20 Å2
2--0.149 Å20 Å2
3----0.298 Å2
Refinement stepCycle: LAST / Resolution: 1.802→28.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 17 72 1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191153
X-RAY DIFFRACTIONr_bond_other_d0.0020.021095
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9421571
X-RAY DIFFRACTIONr_angle_other_deg0.87532525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5695143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81923.33357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90315213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6981510
X-RAY DIFFRACTIONr_chiral_restr0.0870.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02280
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 (%)
1.802-1.8490.3440.23177585595.789
1.849-1.8990.287310.22277382597.455
1.899-1.9540.201430.20273579997.372
1.954-2.0140.233330.18375280297.88
2.014-2.080.254420.1669675497.878
2.08-2.1520.189320.1669073897.832
2.152-2.2330.171380.16766771698.464
2.233-2.3240.184360.16764268898.547
2.324-2.4260.215400.16762467298.81
2.426-2.5440.382250.16960864198.752
2.544-2.680.241230.16259061799.352
2.68-2.8420.154210.17655157699.306
2.842-3.0360.206270.17452755599.82
3.036-3.2760.242220.16848951499.416
3.276-3.5850.198260.16645448199.792
3.585-4.0010.188210.148423444100
4.001-4.6060.154150.14338440099.75
4.606-5.6080.247140.20933334899.713
5.608-7.7960.285110.22626828099.643
7.796-300.2280.21117718997.884
Refinement TLS params.Method: refined / Origin x: 2.6917 Å / Origin y: 32.1058 Å / Origin z: 62.9805 Å
111213212223313233
T0.0125 Å2-0.0003 Å20.0062 Å2-0.0348 Å2-0.0091 Å2--0.0064 Å2
L2.4117 °20.506 °20.2027 °2-3.0092 °20.3768 °2--1.5838 °2
S-0.0278 Å °0.1153 Å °-0.0536 Å °-0.1104 Å °0.0448 Å °-0.0278 Å °-0.0003 Å °0.0225 Å °-0.017 Å °

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