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- PDB-5f5t: Crystal structure of the Prp38-MFAP1 complex of Chaetomium thermo... -

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Basic information

Entry
Database: PDB / ID: 5f5t
TitleCrystal structure of the Prp38-MFAP1 complex of Chaetomium thermophilum
Components(Putative uncharacterized protein) x 2
KeywordsSPLICING / B-specific protein / pre-mRNA splicing / SAH / TRANSCRIPTION
Function / homology
Function and homology information


U2-type spliceosomal complex / precatalytic spliceosome / mRNA splicing, via spliceosome / RNA binding
Similarity search - Function
Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Microfibril-associated/Pre-mRNA processing / Pre-mRNA-splicing factor 38 / PRP38 family
Similarity search - Domain/homology
Pre-mRNA-splicing factor 38 / Micro-fibrillar-associated protein 1 C-terminal domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsUlrich, A.K.C. / Wahl, M.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationWA1126/7-1 Germany
CitationJournal: Structure / Year: 2016
Title: Scaffolding in the Spliceosome via Single alpha Helices.
Authors: Ulrich, A.K.C. / Seeger, M. / Schutze, T. / Bartlick, N. / Wahl, M.C.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)71,5134
Polymers71,5134
Non-polymers00
Water2,504139
1
A: Putative uncharacterized protein
C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)35,7572
Polymers35,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-1 kcal/mol
Surface area16900 Å2
MethodPISA
2
B: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)35,7572
Polymers35,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-0 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.550, 52.150, 104.600
Angle α, β, γ (deg.)90.000, 102.510, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASPASPchain AAA4 - 2187 - 221
2GLUGLUchain BBB4 - 2177 - 220

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Components

#1: Protein Putative uncharacterized protein


Mass: 25617.205 Da / Num. of mol.: 2 / Fragment: NTR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0013190 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0S1D3
#2: Protein Putative uncharacterized protein


Mass: 10139.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0069660 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: G0SHD7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.64 Å3/Da / Density % sol: 66.21 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.2 M ammonium acetate, and 20 % (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.55→95.454 Å / Num. obs: 33726 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rsym value: 0.044 / Net I/σ(I): 17.9
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.9 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rz9

4rz9


Resolution: 2.55→95.454 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 1706 5.06 %Random selection
Rwork0.1955 32013 --
obs0.1969 33719 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 292.36 Å2 / Biso mean: 102.4795 Å2 / Biso min: 35.71 Å2
Refinement stepCycle: final / Resolution: 2.55→95.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 0 139 4557
Biso mean---87.93 -
Num. residues----537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034493
X-RAY DIFFRACTIONf_angle_d0.8146043
X-RAY DIFFRACTIONf_chiral_restr0.033648
X-RAY DIFFRACTIONf_plane_restr0.004799
X-RAY DIFFRACTIONf_dihedral_angle_d14.8571775
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2034X-RAY DIFFRACTION13.221TORSIONAL
12B2034X-RAY DIFFRACTION13.221TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.62510.32291290.31032633276298
2.6251-2.70980.3671480.29222641278999
2.7098-2.80670.30831380.29752635277399
2.8067-2.91910.27831330.26332662279599
2.9191-3.05190.30511330.2262664279799
3.0519-3.21280.24691180.22672668278699
3.2128-3.41410.2681400.20962664280499
3.4141-3.67770.24411420.19312647278998
3.6777-4.04790.16891420.16132692283499
4.0479-4.63360.18111440.15212677282199
4.6336-5.83770.21511720.18232680285299
5.8377-95.52130.20531670.19582750291798
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)
15.09140.9917-4.37775.6961-3.20335.99010.05392.9519-0.5397-0.6439-0.0664-1.64321.30141.0148-0.15291.4287-0.0471-0.20611.8801-0.33281.2588235.9104-29.8655-17.2825
26.54360.3191-0.96624.6216-0.19846.4569-0.26620.5701-0.4047-0.69110.3358-0.40060.0182-0.0823-0.05260.5073-0.1070.07410.5228-0.09090.5026241.366-23.1282-7.3159
31.02030.6585-1.12678.4898-4.32855.7736-0.38370.28850.35680.2616-0.11270.0234-0.46810.34690.38630.46230.0569-0.04380.53260.0060.6231238.0967-13.389-1.169
44.98640.5136-2.8592.4025-0.72064.8897-0.33180.2483-0.4087-0.26850.2211-0.04920.9937-0.40590.0610.4508-0.0537-0.04890.4096-0.07270.5029231.5778-30.98272.3026
57.00730.38850.9331.82410.26725.25860.070.15350.4489-0.09660.02640.590.1373-0.6722-0.0880.38970.0244-0.02340.46550.0230.522222.322-23.4576.7441
64.03311.399-0.05448.49964.81572.90841.1506-0.3741-0.29973.10640.2493-0.50770.248-1.1071-0.81481.75550.01070.01041.55880.12781.23213.3686-24.698333.6192
75.86543.62314.97886.9117-0.59939.61852.1392-2.8892-0.04481.977-0.4297-1.2693-0.6236-1.8194-1.33312.23160.14340.32841.9037-0.2721.5731217.4412-2.392862.7029
84.74350.81890.09884.44650.37891.7128-0.5704-1.14650.14382.00740.52350.8506-0.0773-0.43820.04081.52730.21910.4551.2059-0.00890.829217.8097-13.088157.8732
94.650.83360.52483.22912.3154.91940.0438-0.43320.44080.90220.23630.0432-1.68060.0332-0.2521.4530.02760.10190.7147-0.09270.5326228.9026-6.144450.7169
107.54580.61390.69613.01171.04138.17310.2636-0.24250.44820.29740.08690.2386-0.8958-0.6542-0.37920.81070.18080.10480.4744-0.01350.5139221.9994-7.271138.0645
113.81470.0617-0.52462.51471.51981.14480.75470.00040.5879-0.2904-0.22321.167-1.0198-1.6325-0.43791.00280.41430.21571.20790.09091.0465209.311-3.624435.1181
127.3469-2.90850.34812.07631.61917.8644-0.74540.53910.7984-1.27221.01-0.0867-0.63640.77060.06771.6255-0.0709-0.1371.80470.11841.1947218.8514-5.84418.1816
132.4961-0.8114-2.1269.02014.07113.3346-2.0460.78483.0929-1.15141.9708-0.98910.22361.13-0.1311.1586-0.3177-0.39731.4883-0.08511.4706238.6819-18.507719.7827
146.34780.52643.86020.07320.22951.48080.1104-0.2490.823-0.1386-0.29530.3810.1828-0.54520.2110.52210.069-0.06531.0771-0.05480.8218201.4075-19.52199.5602
152.5215-2.47351.60278.12291.98353.5530.499-2.0976-2.42160.09391.69171.0929-1.9321-0.3887-2.01951.07130.3446-0.03881.4688-0.08321.7268236.6578-12.12229.089
161.8526-0.0587-1.72623.9071.28872.22190.41260.11240.7996-0.1723-0.39081.5065-0.361-1.1668-0.30080.77090.2689-0.02381.1997-0.03321.1023208.0668-10.226422.9075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 30 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 68 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 83 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 142 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 202 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 203 through 218 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 30 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 45 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 46 through 112 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 113 through 169 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 170 through 202 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 203 through 217 )B0
13X-RAY DIFFRACTION13chain 'C' and (resid 215 through 222 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 223 through 277 )C0
15X-RAY DIFFRACTION15chain 'D' and (resid 216 through 222 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 223 through 259 )D0

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