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- PDB-5u50: Crystal structure of citrus MAF1 in space group C 2 2 21 -

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Basic information

Entry
Database: PDB / ID: 5u50
TitleCrystal structure of citrus MAF1 in space group C 2 2 21
ComponentsRepressor of RNA polymerase III transcription
KeywordsTRANSCRIPTION / repressor of RNA polymerase III
Function / homologyRepressor of RNA polymerase III transcription Maf1 / Repressor of RNA polymerase III transcription Maf1 superfamily / Maf1 regulator / negative regulation of transcription by RNA polymerase III / nucleus / Repressor of RNA polymerase III transcription
Function and homology information
Biological speciesCitrus sinensis (sweet orange)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.902 Å
AuthorsSoprano, A.S. / Giuseppe, P.O. / Nascimento, A.F.Z. / Benedetti, C.E. / Murakami, M.T.
CitationJournal: To Be Published
Title: Crystal structure of citrus MAF1 in space group C 2 2 21
Authors: Soprano, A.S. / Giuseppe, P.O. / Nascimento, A.F.Z. / Benedetti, C.E. / Murakami, M.T.
History
DepositionDec 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Repressor of RNA polymerase III transcription
B: Repressor of RNA polymerase III transcription
C: Repressor of RNA polymerase III transcription
D: Repressor of RNA polymerase III transcription


Theoretical massNumber of molelcules
Total (without water)122,7054
Polymers122,7054
Non-polymers00
Water181
1
A: Repressor of RNA polymerase III transcription


Theoretical massNumber of molelcules
Total (without water)30,6761
Polymers30,6761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Repressor of RNA polymerase III transcription


Theoretical massNumber of molelcules
Total (without water)30,6761
Polymers30,6761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Repressor of RNA polymerase III transcription


Theoretical massNumber of molelcules
Total (without water)30,6761
Polymers30,6761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Repressor of RNA polymerase III transcription


Theoretical massNumber of molelcules
Total (without water)30,6761
Polymers30,6761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.165, 228.406, 85.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 53 or resid 73...
21(chain B and (resid 8 through 53 or resid 73...
31(chain C and (resid 8 through 71 or resid 73...
41(chain D and (resid 8 through 53 or resid 59 or resid 78 through 130 or resid 137 through 199))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEU(chain A and (resid 8 through 53 or resid 73...AA8 - 5349 - 94
12SERSERSERSER(chain A and (resid 8 through 53 or resid 73...AA73114
13LYSLYSGLUGLU(chain A and (resid 8 through 53 or resid 73...AA78 - 130119 - 171
14LEULEUASPASP(chain A and (resid 8 through 53 or resid 73...AA137 - 162178 - 203
15ALAALAASNASN(chain A and (resid 8 through 53 or resid 73...AA173 - 199214 - 240
21PROPROLEULEU(chain B and (resid 8 through 53 or resid 73...BB8 - 5349 - 94
22SERSERSERSER(chain B and (resid 8 through 53 or resid 73...BB73114
23LYSLYSGLUGLU(chain B and (resid 8 through 53 or resid 73...BB78 - 130119 - 171
24LEULEUASPASP(chain B and (resid 8 through 53 or resid 73...BB137 - 162178 - 203
25ALAALAASNASN(chain B and (resid 8 through 53 or resid 73...BB173 - 199214 - 240
31PROPROLEULEU(chain C and (resid 8 through 71 or resid 73...CC8 - 7149 - 112
32SERSERSERSER(chain C and (resid 8 through 71 or resid 73...CC73114
33LYSLYSGLUGLU(chain C and (resid 8 through 71 or resid 73...CC78 - 130119 - 171
34LEULEUASPASP(chain C and (resid 8 through 71 or resid 73...CC137 - 162178 - 203
35ALAALAASNASN(chain C and (resid 8 through 71 or resid 73...CC173 - 199214 - 240
41PROPROLEULEU(chain D and (resid 8 through 53 or resid 59 or resid 78 through 130 or resid 137 through 199))DD8 - 5349 - 94
42SERSERSERSER(chain D and (resid 8 through 53 or resid 59 or resid 78 through 130 or resid 137 through 199))DD59100
43LYSLYSGLUGLU(chain D and (resid 8 through 53 or resid 59 or resid 78 through 130 or resid 137 through 199))DD78 - 130119 - 171
44LEULEUASNASN(chain D and (resid 8 through 53 or resid 59 or resid 78 through 130 or resid 137 through 199))DD137 - 199178 - 240

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Components

#1: Protein
Repressor of RNA polymerase III transcription


Mass: 30676.334 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus sinensis (sweet orange) / Gene: MAF1 / Production host: Escherichia coli (E. coli) / References: UniProt: G9I821
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1 M sodium formate, 0.1 M sodium acetate pH 4.6, dioxane 1%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.9→19.977 Å / Num. obs: 30801 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.835 % / Biso Wilson estimate: 83.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.086 / Χ2: 1.021 / Net I/σ(I): 15.47 / Num. measured all: 179725
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-3.085.4050.8451.9926083491148260.8130.93698.3
3.08-3.296.1530.4723.9228517463846350.9480.51699.9
3.29-3.555.9780.2357.4525783431443130.9820.257100
3.55-3.895.8740.12712.2323491400539990.9940.13999.9
3.89-4.345.9660.07618.9421626362836250.9980.08499.9
4.34-5.015.8590.05227.218836322532150.9980.05699.7
5.01-6.125.8470.05427.3316080275927500.9980.05999.7
6.12-8.595.7610.04234.9512437216321590.9990.04699.8
8.59-19.9775.3730.03147.696872130812790.9990.03497.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.902→19.977 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 32.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 2709 4.64 %
Rwork0.2221 55701 -
obs0.2237 58410 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 212.65 Å2 / Biso mean: 113.2507 Å2 / Biso min: 50.52 Å2
Refinement stepCycle: final / Resolution: 2.902→19.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5689 0 0 1 5690
Biso mean---78.8 -
Num. residues----680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045837
X-RAY DIFFRACTIONf_angle_d0.7667873
X-RAY DIFFRACTIONf_chiral_restr0.047843
X-RAY DIFFRACTIONf_plane_restr0.005977
X-RAY DIFFRACTIONf_dihedral_angle_d15.8763435
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2937X-RAY DIFFRACTION14.444TORSIONAL
12B2937X-RAY DIFFRACTION14.444TORSIONAL
13C2937X-RAY DIFFRACTION14.444TORSIONAL
14D2937X-RAY DIFFRACTION14.444TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9016-2.95420.46691430.42662855299897
2.9542-3.01090.44341350.38642827296298
3.0109-3.07210.39761380.35932970310898
3.0721-3.13870.35391260.348429163042100
3.1387-3.21140.3561730.34782932310599
3.2114-3.29130.28851710.283629303101100
3.2913-3.37990.35131780.26152896307499
3.3799-3.47890.28611630.249229353098100
3.4789-3.59050.2971430.230429073050100
3.5905-3.71810.28781790.220729343113100
3.7181-3.86590.27841390.216929323071100
3.8659-4.04050.23121620.21529403102100
4.0405-4.25160.21861130.187229543067100
4.2516-4.51510.22211010.16432976307799
4.5151-4.8590.21211360.160629483084100
4.859-5.33950.22081380.187129593097100
5.3395-6.09290.2891230.233129693092100
6.0929-7.60540.26211060.252729823088100
7.6054-19.97720.20051420.19352939308199
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)
12.3993-0.40131.0264.4407-0.94994.2755-0.18820.2438-0.3075-0.1550.0627-0.1415-0.20970.14970.11290.7882-0.09230.21630.4511-0.10870.703812.618714.166810.1542
23.79260.6357-0.10883.17110.12913.1918-0.40730.31860.1456-1.15110.1460.0292-0.40080.05280.2181.5428-0.2349-0.0140.62870.05410.685717.617846.2069-3.0171
32.1221-0.1325-0.01034.3071-0.97052.10070.4416-0.3833-0.10230.6086-0.5495-0.6811-0.39120.32950.09341.3196-0.52220.03340.98150.07240.964148.149741.1194-18.82
42.47581.55360.9194.39710.49743.65330.108-0.096-0.4355-0.1108-0.2951-0.9698-0.09760.63120.2240.8214-0.0538-0.05640.76740.18281.135742.37617.0857-20.7053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 8 through 199)A8 - 199
2X-RAY DIFFRACTION2(chain 'B' and resid 8 through 201)B8 - 201
3X-RAY DIFFRACTION3(chain 'C' and resid 8 through 200)C8 - 200
4X-RAY DIFFRACTION4(chain 'D' and resid 8 through 199)D8 - 199

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