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- PDB-7r5z: Monocot chimeric jacalin JAC1 from Oryza sativa: dirigent domain ... -

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Basic information

Entry
Database: PDB / ID: 7r5z
TitleMonocot chimeric jacalin JAC1 from Oryza sativa: dirigent domain (crystal form 1)
ComponentsDirigent protein
KeywordsPLANT PROTEIN / Monocot chimeric jacalin / Dirigent protein / Lectin / Pathogen resistance
Function / homology
Function and homology information


phenylpropanoid biosynthetic process / apoplast / carbohydrate binding / metal ion binding
Similarity search - Function
Dirigent protein / Dirigent-like protein / Allene oxide cyclase/Dirigent protein / Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily
Similarity search - Domain/homology
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHuwa, N. / Classen, T. / Weiergraeber, O.H.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)369034981 Germany
German Research Foundation (DFG)SCHA 631/10-1 Germany
CitationJournal: Biomolecules / Year: 2022
Title: The Crystal Structure of the Defense Conferring Rice Protein Os JAC1 Reveals a Carbohydrate Binding Site on the Dirigent-like Domain.
Authors: Huwa, N. / Weiergraber, O.H. / Fejzagic, A.V. / Kirsch, C. / Schaffrath, U. / Classen, T.
History
DepositionFeb 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 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: Dirigent protein
B: Dirigent protein
C: Dirigent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5739
Polymers52,3563
Non-polymers2176
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.990, 87.360, 93.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Dirigent protein /


Mass: 17452.025 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: JAC1, LOC_Os12g14440, Os12g0247700, OSNPB_120247700 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q306J3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG 3350, calcium chloride, Tris-HCl, dithiothreitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.75→43.68 Å / Num. obs: 41085 / % possible obs: 99.4 % / Redundancy: 13.72 % / Biso Wilson estimate: 31.87 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.11
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 13 % / Mean I/σ(I) obs: 0.69 / Num. unique obs: 2914 / CC1/2: 0.346 / % possible all: 97.6

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Processing

Software
NameVersionClassification
XDSdata reduction
MoRDaphasing
PHENIX1.19.2_4158refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OOD

6ood


Resolution: 1.75→43.68 Å / SU ML: 0.2553 / Cross valid method: FREE R-VALUE / Phase error: 27.3662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 2055 5.01 %
Rwork0.191 38995 -
obs0.1929 41050 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.22 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 6 120 3347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633434
X-RAY DIFFRACTIONf_angle_d0.8634683
X-RAY DIFFRACTIONf_chiral_restr0.0588523
X-RAY DIFFRACTIONf_plane_restr0.0057614
X-RAY DIFFRACTIONf_dihedral_angle_d13.92711169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.38131320.39482492X-RAY DIFFRACTION97.51
1.79-1.840.33991330.33572539X-RAY DIFFRACTION98.93
1.84-1.890.32141370.29192592X-RAY DIFFRACTION99.49
1.89-1.940.30951340.28592559X-RAY DIFFRACTION99.7
1.94-20.28881370.27852584X-RAY DIFFRACTION99.38
2-2.070.27261350.25422560X-RAY DIFFRACTION99.67
2.07-2.160.27121360.22642594X-RAY DIFFRACTION99.67
2.16-2.260.24591360.20642578X-RAY DIFFRACTION99.52
2.26-2.380.221380.19362605X-RAY DIFFRACTION99.75
2.38-2.520.24691370.20672606X-RAY DIFFRACTION99.78
2.52-2.720.25621380.20822626X-RAY DIFFRACTION99.96
2.72-2.990.24921380.19982609X-RAY DIFFRACTION99.96
2.99-3.430.23681350.18042567X-RAY DIFFRACTION96.71
3.43-4.310.19241400.14992671X-RAY DIFFRACTION99.93
4.31-43.680.19051490.1642813X-RAY DIFFRACTION99.87
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)
11.726315927740.108448771881.578170245621.579392993380.0799644848084.00015150032-0.0899799137399-0.1070664948410.0225048863695-0.04609312542710.182282888539-0.5670850614560.2380324093771.15945731831-0.4672604889490.318838716240.0436835161095-0.01142777676230.738038857139-0.1392569839850.49719228269452.618658440639.633197458147.3976091806
20.2836801570520.547860379451-0.3464717518142.20188438149-0.09996121600696.11356803018-0.09301893766110.368363669774-0.032535137663-0.3733718768670.0990882182519-0.01947879872040.126603234473-0.113967056366-0.0416105797690.251951689154-0.01412675794170.01181898130070.324379608802-0.01809775226970.25842651255241.885126009239.724033015146.075822872
30.98147933743-1.586541313991.715927021752.57922625384-2.765830665372.978784268091.133866279882.11744587409-1.00260012958-0.395285239630.805353084667-2.298595446072.744105465853.0810540175-1.183812767681.139219673360.429052461488-0.02719875966831.277660578-0.2631321331780.94832483876257.373050048229.432124878854.9211371796
46.972372529141.086786327080.5817407362973.478727431312.540812011851.89999450049-0.08966675815640.1910642922460.0553562013375-0.272583793753-0.0677194947636-0.352056120416-0.2576616584951.108413054550.2650389027910.22991791692-0.008494206834660.04165365971370.504191054659-0.01508787819930.32660835374649.963089325943.24851845253.4031039687
54.376260624571.78788622305-0.5094000809923.770918937110.06974006455052.68179804605-0.3603048036940.627106599849-0.0645495222295-0.5684795285050.289551657124-0.20507654272-0.1231753544361.330630003360.110282653690.303520074162-0.02681438310990.05642781356020.679129232955-0.03040168310620.40027429395352.79072196143.466470468645.2502627928
61.00790566699-0.498614813927-1.58023331142.01201002523-0.4266575408048.93686051905-0.1956437109771.094560921320.509668719897-0.0583183564273-0.6505753571750.876466406235-1.00968514352-0.03861499698340.4888610239080.436974311277-0.0352956912074-0.05725388479951.39570479047-0.168012862920.85853079462164.207727780246.783394630460.3601889545
76.09186518132-2.6154906137-3.163777965342.05442460677-0.5542522438857.259117149060.527998249903-0.542556895161.40021414055-0.05621361483150.16167958929-0.872905808872-2.833838315750.4736400257370.5770440632811.05088190380.1221156138650.08352273595180.406879587249-0.09467682971870.65263186319640.397068434563.101324443462.5434144611
83.70781405185-0.1579466629210.4728214852843.359676032520.7294453867943.56346223020.3438590860930.2866919368890.4981498511020.300202910754-0.005346406270830.824149362641-1.44153184051-1.982562177420.9224831574140.6599527561360.3675159910880.08600763783650.7820707410030.06111028766340.44612499743726.940177970552.995661908855.7301486656
93.108618855161.894626482121.095993701362.349860167021.884218284961.54583767780.0652469980773-0.188980210082-0.295481421088-0.030241258697-0.1661337640090.0517268158676-0.830213636199-0.6904571290890.05294922957480.3428866704650.109477966396-0.002149249972790.3563912361520.005647603764940.28141044797134.511409711851.300827475457.4433589675
107.69282177131-0.09104278731344.318854652836.609505855423.846150879654.724737227620.00138888816311.808457204263.26434797443-0.298379748982-2.1969726325-0.552954549798-2.61535380011.59930262908-0.7338538465671.98654213468-0.2272698823270.3168468401930.9708465165990.3017680167711.1131001745745.988240658663.35082847850.2417755806
114.922664152461.589805096572.674363091696.01183139405-0.9611530203043.605880946430.154766926382-0.4988876470620.696520824465-0.2155311679090.169640006370.0586255192005-1.712223126530.0842920494015-0.07968234515890.432074482007-0.03754185273440.01592244201060.18149782979-0.05362035978140.2990051600440.639097273552.596042788262.1348092432
121.73789460073-0.567944830882.644259903012.75594362338-2.320446731535.74650820192-0.50171972404-0.637703206233-0.371103921505-0.004899544338020.452649979310.859775466294-2.38240722886-1.05555222278-0.01673245835370.7618604130430.08132675312060.02095350231050.39918326273-0.1176975788490.45581935054537.159667425558.267694168565.7240553106
130.1638604372210.34294289277-0.6441436159521.66618859296-0.6247074079613.118868517380.6612070271690.645013846574-0.084389155779-0.377801448314-0.28233622711-0.287629238938-1.447398299370.1034747606820.3577240341270.6771090810180.09975558633310.1074253351210.52587371107-0.1094331588180.4881223381839.497442202758.944323874362.889491854
143.37763787951-3.009881512512.112752644083.22852704750.08303037420768.535646161680.358896684717-0.464881450589-0.5828425158220.9012936685380.519031347351-0.6119206800261.70216594279-0.0450071661655-0.7996459351620.993636975153-0.334892621133-0.4006676228481.061367597660.1148044791150.63877675178950.132503655639.994005409578.5739846067
156.27489056685-0.175183075345-4.238592820884.142401323271.800121167293.84548679509-0.7491287800960.0482764155443-0.2704013911270.5774124826550.4230480627820.3320218534671.75444075158-1.302232377770.03336423607780.784391790138-0.207938414463-0.007661464500910.4591481417720.06903508119160.43807792812231.695609934727.201587092369.8295637707
162.60578755663-0.00619285338414-0.5073702971992.77217196501-0.1444950692072.19478828796-0.0718443383285-0.0386382425531-0.34495976310.152405917801-0.0508292309720.1070070014561.13624316175-0.725052747020.06124669590980.419187070651-0.1257119758180.01549570573910.388689664180.00218514216770.39288649883734.660170654532.840239122463.1872923036
172.916956592871.80487538206-2.375273247777.684935384330.7783354506492.688629870940.06457463990340.0449154624785-0.4114968063090.321765119967-0.315514754888-0.4733287431370.760792772089-0.2948517508640.1132804420450.4318569573867.24823031787E-50.02177017880930.734965275453-0.0318213191520.40657453025436.982084381443.732116581180.9467771439
184.74714613962-0.718939943546-1.182123359424.139695534753.95489059246.31970868573-0.221910151032-0.165435268852-0.2141106699950.862821325528-0.04457607389270.3263414601710.8832870437030.1416391794250.2439656493070.2722244323020.0551694620090.0085390532870.2575727511010.05947355652480.22133055786642.908955226835.221101529563.769233249
194.321630630330.276807421091-0.2637011364581.51294786952-1.023767763374.93195344653-0.1054599071-0.450221543967-0.489285433550.5976578976610.0690554225753-0.4811089283410.8002860247610.6670372553150.206034677690.3664882291750.061905360560.00484971546240.4199371196360.0648311757210.33014243209645.444386070936.064362656669.7600708412
202.508453627595.911780261210.541118221117.587549854620.9820989173695.03107416385-0.688790145714-0.694311660707-0.813854081275-0.05584395927210.297822764783-0.2176581697090.6182763673270.641086341804-0.04396624565580.8059175812430.0986736330266-0.1100092574110.5312462814190.04016119639660.49706347124542.724596799831.243249700171.9468142955
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 14 through 41 )AA14 - 411 - 28
22chain 'A' and (resid 42 through 93 )AA42 - 9329 - 80
33chain 'A' and (resid 94 through 101 )AA94 - 10181 - 88
44chain 'A' and (resid 102 through 124 )AA102 - 12489 - 111
55chain 'A' and (resid 125 through 155 )AA125 - 155112 - 142
66chain 'B' and (resid 6 through 18 )BE6 - 181 - 13
77chain 'B' and (resid 19 through 30 )BE19 - 3014 - 25
88chain 'B' and (resid 31 through 70 )BE31 - 7026 - 65
99chain 'B' and (resid 71 through 93 )BE71 - 9366 - 88
1010chain 'B' and (resid 94 through 101 )BE94 - 10189 - 96
1111chain 'B' and (resid 102 through 124 )BE102 - 12497 - 119
1212chain 'B' and (resid 125 through 138 )BE125 - 138120 - 133
1313chain 'B' and (resid 139 through 159 )BE139 - 159134 - 154
1414chain 'C' and (resid 17 through 25 )CG17 - 251 - 9
1515chain 'C' and (resid 26 through 38 )CG26 - 3810 - 22
1616chain 'C' and (resid 39 through 93 )CG39 - 9323 - 77
1717chain 'C' and (resid 94 through 101 )CG94 - 10178 - 85
1818chain 'C' and (resid 102 through 112 )CG102 - 11286 - 96
1919chain 'C' and (resid 113 through 138 )CG113 - 13897 - 122
2020chain 'C' and (resid 139 through 155 )CG139 - 155123 - 139

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