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- PDB-5mpx: Crystal structure of Arabidopsis thaliana RNA editing factor MORF... -

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Basic information

Entry
Database: PDB / ID: 5mpx
TitleCrystal structure of Arabidopsis thaliana RNA editing factor MORF1, space group P2(1)
ComponentsMultiple organellar RNA editing factor 1, mitochondrial
KeywordsPLANT PROTEIN / NFLD-related fold
Function / homology
Function and homology information


mitochondrial mRNA modification / chloroplast RNA modification / mitochondrial RNA modification / cytidine to uridine editing / chloroplast / mRNA processing / protein dimerization activity / mitochondrion
Similarity search - Function
MORF/ORRM1/DAG-like / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily
Similarity search - Domain/homology
Multiple organellar RNA editing factor 1, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.938 Å
AuthorsHaag, S. / Schindler, M. / Berndt, L. / Brennicke, A. / Takenaka, M. / Weber, G.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Crystal structures of the Arabidopsis thaliana organellar RNA editing factors MORF1 and MORF9.
Authors: Haag, S. / Schindler, M. / Berndt, L. / Brennicke, A. / Takenaka, M. / Weber, G.
History
DepositionDec 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Jan 17, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multiple organellar RNA editing factor 1, mitochondrial
B: Multiple organellar RNA editing factor 1, mitochondrial
C: Multiple organellar RNA editing factor 1, mitochondrial
D: Multiple organellar RNA editing factor 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,74211
Polymers52,0704
Non-polymers6727
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-174 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.892, 69.818, 69.324
Angle α, β, γ (deg.)90.000, 108.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Multiple organellar RNA editing factor 1, mitochondrial / RNA editing-interacting protein 8


Mass: 13017.480 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MORF1, RIP8, At4g20020 / Production host: Escherichia coli (E. coli) / References: UniProt: O49429
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0,1 M Bicine, pH 9.0 and 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.771 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.14
ReflectionResolution: 1.938→50 Å / Num. obs: 44847 / % possible obs: 97.7 % / Redundancy: 6.1 % / Rsym value: 0.11 / Net I/σ(I): 11.8
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.32 / Num. unique all: 2880 / CC1/2: 0.569 / Rsym value: 0.63 / % possible all: 83.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MPW
Resolution: 1.938→34.807 Å / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.38
RfactorNum. reflection% reflection
Rfree0.1917 1116 2.49 %
Rwork0.1628 --
obs0.1631 44844 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.21 Å2 / Biso mean: 32.3157 Å2 / Biso min: 12.35 Å2
Refinement stepCycle: final / Resolution: 1.938→34.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 35 416 4095
Biso mean--55.64 34.52 -
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073758
X-RAY DIFFRACTIONf_angle_d0.835090
X-RAY DIFFRACTIONf_chiral_restr0.051528
X-RAY DIFFRACTIONf_plane_restr0.005668
X-RAY DIFFRACTIONf_dihedral_angle_d16.5782242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9429-2.03120.27631300.24155231536192
2.0312-2.13820.26471340.21865374550894
2.1382-2.2720.25321330.2135382551594
2.272-2.44720.2231340.19735452558695
2.4472-2.6930.2191360.18315490562696
2.693-3.08160.19731380.1735549568797
3.0816-3.87830.18481390.14085591573097
3.8783-20.65960.131400.11715623576396
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.0867-4.2644-3.37253.30571.73921.7135-0.1029-0.4438-0.36360.00830.02910.1684-0.13170.3381-0.00460.2125-0.05470.01130.2419-0.02510.1752-0.18136.3132-22.188
23.12310.5328-0.49923.0829-0.50392.67750.1645-0.36720.09450.1764-0.1831-0.0172-0.28060.09670.0240.1471-0.0211-0.02150.2277-0.00370.110523.51265.3977-35.8797
35.70612.8595-1.14252.11321.56487.830.2677-0.7543-0.46130.3851-0.28150.26160.6819-0.01580.1090.2212-0.0493-0.08060.27430.06880.239233.0306-1.9778-30.8961
40.008-0.05720.06910.3884-0.51210.86160.06820.7149-0.5-0.07770.1202-0.15510.0788-0.0888-0.11160.2224-0.0184-0.00220.3044-0.0790.2303-7.4257-5.254-32.1953
53.28730.91630.71334.4242-0.14375.28210.04580.4758-0.3601-0.3643-0.0148-0.21990.15760.2620.02370.19370.044-0.00360.1938-0.04560.127218.7545-8.5895-52.68
63.38820.4562-0.00483.5975-0.30943.6778-0.02750.1047-0.0054-0.06080.05420.30430.0065-0.4407-0.01640.14870.0351-0.02660.2512-0.03580.10379.3147-4.1889-48.8712
73.17342.8913-4.96458.7953-5.46128.03490.3154-0.24550.5431-0.0438-0.20230.2172-0.4139-0.18-0.0240.29450.097-0.07630.307-0.04390.223110.45151.8895-60.3656
80.0671-0.2463-0.34970.98341.29581.78590.0667-0.1676-0.10190.204-0.01960.12630.07450.0376-0.01290.2025-0.00170.00760.26980.01190.235711.335-6.8646-32.1536
90.73350.104-0.81183.8313-0.31614.8776-0.1694-0.1994-0.21470.4780.09120.48910.4895-0.2180.04270.2706-0.03130.06740.20860.02520.1954-11.7238-8.5767-11.8709
103.9094-0.2051-0.8044.0269-0.64292.8215-0.1303-0.14260.06640.03230.0504-0.016-0.03510.41650.04660.2023-0.0118-0.02330.2050.03010.0654-5.1194-3.0078-18.6656
115.9583-3.9259-1.9975.92284.50384.9279-0.0780.1140.4325-0.0142-0.0835-0.3993-0.8110.22120.1650.52670.0291-0.04360.35160.02270.1261-6.6837-1.0074-2.6471
125.1398-0.1275-0.58590.05560.0470.083-0.1362-0.2910.1278-0.21270.0820.01580.05770.08120.02010.25810.01580.01440.2044-0.01550.21546.03527.3046-39.5984
134.45220.73490.44744.6052-2.32972.8516-0.04-0.85150.34850.7889-0.04230.5441-0.3796-0.5758-0.05850.2619-0.01160.02620.3508-0.11450.2792-20.37798.7998-18.5045
148.19751.3451-5.28435.3617-2.73888.4340.1172-0.3850.62960.3134-0.33090.6828-0.2472-0.41280.07510.18310.0294-0.02530.2417-0.13880.2735-23.270313.2895-25.1877
153.62371.2730.24353.09190.20112.9862-0.01250.12510.0678-0.0925-0.05910.0887-0.0033-0.1640.05460.1170.013-0.02440.132-0.02480.1521-15.45867.0012-29.9716
164.0132.2216-1.11877.333-2.16475.70310.05790.1699-0.67-0.14480.118-0.2410.39780.2381-0.06650.17920.0227-0.12420.2218-0.0410.3905-27.02311.8754-33.8548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 76 through 88 )A76 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 179 )A89 - 179
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 190 )A180 - 190
4X-RAY DIFFRACTION4chain 'B' and (resid 76 through 88 )B76 - 88
5X-RAY DIFFRACTION5chain 'B' and (resid 89 through 120 )B89 - 120
6X-RAY DIFFRACTION6chain 'B' and (resid 121 through 179 )B121 - 179
7X-RAY DIFFRACTION7chain 'B' and (resid 180 through 190 )B180 - 190
8X-RAY DIFFRACTION8chain 'C' and (resid 76 through 88 )C76 - 88
9X-RAY DIFFRACTION9chain 'C' and (resid 89 through 147 )C89 - 147
10X-RAY DIFFRACTION10chain 'C' and (resid 148 through 179 )C148 - 179
11X-RAY DIFFRACTION11chain 'C' and (resid 180 through 190 )C180 - 190
12X-RAY DIFFRACTION12chain 'D' and (resid 76 through 88 )D76 - 88
13X-RAY DIFFRACTION13chain 'D' and (resid 89 through 104 )D89 - 104
14X-RAY DIFFRACTION14chain 'D' and (resid 105 through 120 )D105 - 120
15X-RAY DIFFRACTION15chain 'D' and (resid 121 through 179 )D121 - 179
16X-RAY DIFFRACTION16chain 'D' and (resid 180 through 190 )D180 - 190

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