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- PDB-7qb6: Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in co... -

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Basic information

Entry
Database: PDB / ID: 7qb6
TitleCrystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with 3-carboxybenzophenone
ComponentsNodulin-13
KeywordsPLANT PROTEIN / Patogenesis Related protein / PR-10 protein / nodulin-13 / cytokinin signaling pathway / nodulation / 3-carboxybenzophenone / photooxidation
Function / homology
Function and homology information


nodulation / cytokinin-activated signaling pathway / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity
Similarity search - Function
Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START-like domain superfamily
Similarity search - Domain/homology
3-benzoylbenzoic acid / MALONATE ION / Nodulin-13
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsGrzechowiak, M. / Ignasiak, M. / Nowicka-Bauer, K. / Marciniak, B. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO_2017/27/B/ST/00375 Poland
Citation
Journal: Free Radic Biol Med / Year: 2023
Title: Does the presence of ground state complex between a PR-10 protein and a sensitizer affect the mechanism of sensitized photo-oxidation?
Authors: Ignasiak-Kciuk, M. / Nowicka-Bauer, K. / Grzechowiak, M. / Ravnsborg, T. / Frackowiak, K. / Jensen, O.N. / Jaskolski, M. / Marciniak, B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The landscape of cytokinin binding by a plant nodulin.
Authors: Ruszkowski, M. / Szpotkowski, K. / Sikorski, M. / Jaskolski, M.
History
DepositionNov 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nodulin-13
B: Nodulin-13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9884
Polymers37,6602
Non-polymers3282
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-7 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.803, 102.803, 223.386
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid -4 through 159)
d_2ens_1(chain "B" and resid -4 through 159)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILEASNA1 - 164
d_21ens_1ILEASNC1 - 164

NCS oper: (Code: givenMatrix: (0.120590891633, -0.0449602411824, 0.991683625744), (-0.00281267745899, -0.998985311995, -0.0449492520852), (0.992698305479, 0.0026311842066, -0.120594988159)Vector: -57. ...NCS oper: (Code: given
Matrix: (0.120590891633, -0.0449602411824, 0.991683625744), (-0.00281267745899, -0.998985311995, -0.0449492520852), (0.992698305479, 0.0026311842066, -0.120594988159)
Vector: -57.5070231483, 143.793152308, 68.2659009)

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Components

#1: Protein Nodulin-13 / MtN13 / Pathogenesis-related PR10-like protein


Mass: 18830.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: N13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold / References: UniProt: P93330
#2: Chemical ChemComp-A8I / 3-benzoylbenzoic acid / 3-(phenylcarbonyl)benzoic acid / benzophenone-3-carboxylic acid / 3-carboxybenzophenone


Mass: 226.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.95 Å3/Da / Density % sol: 68.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 M SODIUM MALONATE, protein 10 mg/ml, 3-carboxybenzophenone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.52→19.92 Å / Num. obs: 20540 / % possible obs: 99.5 % / Redundancy: 26.3 % / Biso Wilson estimate: 77.65 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.076 / Net I/σ(I): 33.93
Reflection shellResolution: 2.52→2.66 Å / Redundancy: 26.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 3210 / CC1/2: 0.84 / Rrim(I) all: 0.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jhg

4jhg


Resolution: 2.52→19.92 Å / SU ML: 0.3588 / Cross valid method: FREE R-VALUE / Phase error: 27.4873
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.223 984 4.8 %
Rwork0.1952 19534 -
obs0.1965 20518 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.65 Å2
Refinement stepCycle: LAST / Resolution: 2.52→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 24 16 2620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842658
X-RAY DIFFRACTIONf_angle_d1.00233593
X-RAY DIFFRACTIONf_chiral_restr0.0567394
X-RAY DIFFRACTIONf_plane_restr0.0057466
X-RAY DIFFRACTIONf_dihedral_angle_d23.0134985
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.922722005973 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.660.34721360.31012712X-RAY DIFFRACTION99.23
2.66-2.820.31191380.31092741X-RAY DIFFRACTION99.79
2.82-3.040.32541400.2742770X-RAY DIFFRACTION99.97
3.04-3.340.27451380.24462757X-RAY DIFFRACTION99.79
3.34-3.820.23411400.19892785X-RAY DIFFRACTION99.93
3.82-4.810.17771430.16832818X-RAY DIFFRACTION99.97
4.81-19.920.20331490.16652951X-RAY DIFFRACTION99.94
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)
15.558584543191.98302516534-5.287149701562.53163063294-3.402779049156.09166852676-0.0524272848023-0.4104132750830.162309720912-0.185147374729-0.0438747870334-0.0202454687133-0.4370441154761.02599910242-0.3012391905380.576904800284-0.0477911599446-0.1079627963330.937083700056-0.01943266463030.74373200887317.09035178467.331984455581.1189738514
26.641665893950.749283783227-2.024079641464.11827305891-0.536270053253.79447706423-0.248157824724-0.423121517168-0.7177981180720.06695614614940.151042667388-0.4934963788240.189134327350.3497360999670.2385542859270.4346882397410.0545678572837-0.005926511574740.8163948769710.04480849307780.66084931557714.689793186249.102870861692.6663752885
34.348334708124.45811835691-3.409598176155.2816124181-4.144924741827.55277963959-1.132776219253.07522795254-2.13367126221-1.836317505530.5467611109630.657078447880.453229852582-1.641850231230.5194805507141.02245266375-0.134534377932-0.04288916722331.41042476379-0.2697183324661.1570391890312.94464245355.354077726675.152733787
46.24475737412-1.98931231693-7.153488993023.828717071881.416773653879.24363503075-0.0466761835104-0.567966369970.3271025898340.3145046293590.290328439022-0.201234748994-0.241944232530.930349087191-0.2650846608520.402360147167-0.0326418846245-0.1044328185570.745676710523-0.03808282318270.58120888244515.074863723362.947151664992.6259670696
51.150875585330.631477151106-0.6386857086350.356300133964-0.3700838941360.678266560919-0.5093594867252.78973501324-0.648380900429-1.397741793250.8081054505850.0296229249331-0.738543749538-1.59261418269-0.6357563622261.5976708524-0.16073163199-0.03768387991522.104353030380.2241764435490.9904117514112.583403705966.510326116269.6034280213
65.146209221663.52214924487-5.070972295556.87753604873-2.66304738939.815654270940.0228177745598-0.3501261363230.00148608095686-0.129404334623-0.2463142831280.0533336586065-0.02479387062730.2545498426140.2937889272790.3517442189020.0692899144146-0.03986926970860.824751773508-0.09723690603070.6217063261625.7440016552855.954860704594.2887235288
74.31265531140.394637882316-2.15250516862.72467129844-0.5848720748584.09287037514-0.157205978121-0.33683869142-0.441520891528-0.132999491716-0.217464246008-0.386523599038-0.3833765211890.9755768214480.235983001610.779484382949-0.117379373566-0.1716497504641.075771451760.07098323071530.60689523284731.048679591677.159835830773.1155443085
83.79283138384-0.886243133814-1.728597615264.45054055314-0.02503041679275.570845298960.226711349474-0.333061466620.3018915799590.256821401165-0.237116782174-0.367520328898-1.466974577430.9736306014710.02633054095511.2276444076-0.330229059597-0.1895443088620.995033148746-0.03685176880170.72468797491732.044775658991.738729307172.207899682
93.531841830121.81871848548-2.38849943386.20527604967-1.119851251596.42977478999-0.06839383050510.3499493722310.4093826817820.1312558703080.08872311171380.340038639029-0.982231170187-0.06638686476990.01442722639460.812260560264-0.056648983135-0.1618332045440.9589532585370.08169906088280.51600440888828.206172651379.236519512372.2576104793
108.171118355771.8505119261-5.527423701684.70933481987-2.333849931358.78035227347-0.2044712635831.66486485890.630656662877-0.2191980732110.5125743337520.509883315671-0.509272692424-0.216640513037-0.1310629239260.962413879764-0.00769582538345-0.1613127908161.000362473390.173518916030.75721756416929.719687659981.888227322664.5535383084
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -4 through 12 )AA-4 - 121 - 17
22chain 'A' and (resid 13 through 84 )AA13 - 8418 - 89
33chain 'A' and (resid 85 through 96 )AA85 - 9690 - 101
44chain 'A' and (resid 97 through 123 )AA97 - 123102 - 128
55chain 'A' and (resid 124 through 130 )AA124 - 130129 - 135
66chain 'A' and (resid 131 through 159 )AA131 - 159136 - 164
77chain 'B' and (resid -4 through 23 )BC-4 - 231 - 28
88chain 'B' and (resid 24 through 84 )BC24 - 8429 - 89
99chain 'B' and (resid 85 through 123 )BC85 - 12390 - 128
1010chain 'B' and (resid 124 through 159 )BC124 - 159129 - 164

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