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- PDB-7rbp: Medicago truncatula D-1-piperideine-2-carboxylic acid reductase -

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Basic information

Entry
Database: PDB / ID: 7rbp
TitleMedicago truncatula D-1-piperideine-2-carboxylic acid reductase
ComponentsOrnithine cyclodeaminase/mu-crystallin
KeywordsOXIDOREDUCTASE / pipecolic acid / N-hydroxy-pipecolic acid / systemic acquired resistance / plant defense hormone / Mu-crystallin
Function / homology
Function and homology information


Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ornithine cyclodeaminase/mu-crystallin
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTorrens-spence, M.P. / Weng, J.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Pipecolic acid pathway is conserved in systemic acquired resistance between dicotyledon and monocotyledon plants
Authors: Torrens-Spence, M.P. / Weng, J.K.
History
DepositionJul 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Ornithine cyclodeaminase/mu-crystallin
B: Ornithine cyclodeaminase/mu-crystallin


Theoretical massNumber of molelcules
Total (without water)72,9332
Polymers72,9332
Non-polymers00
Water1,29772
1
A: Ornithine cyclodeaminase/mu-crystallin

B: Ornithine cyclodeaminase/mu-crystallin


Theoretical massNumber of molelcules
Total (without water)72,9332
Polymers72,9332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y+1/2,-z+1/21
Buried area2720 Å2
ΔGint-26 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.140, 83.665, 113.810
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 Ornithine cyclodeaminase/mu-crystallin


Mass: 36466.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11419735, MTR_1g099620 / Production host: Escherichia coli (E. coli) / References: UniProt: B7FJU0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.25 M Ammonium Tartrate Dibasic, 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→67.41 Å / Num. obs: 45056 / % possible obs: 98.84 % / Redundancy: 2 % / Biso Wilson estimate: 55.74 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01401 / Rpim(I) all: 0.01401 / Rrim(I) all: 0.01401 / Net I/σ(I): 16.22
Reflection shellResolution: 2.104→2.179 Å / Redundancy: 2 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 4425 / CC1/2: 0.291 / CC star: 0.671 / Rpim(I) all: 0.685 / Rrim(I) all: 0.658 / % possible all: 99.68

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BV9

4bv9


Resolution: 2.1→67.41 Å / SU ML: 0.3684 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.8075
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.272 1987 4.46 %
Rwork0.252 42595 -
obs0.2529 44582 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.45 Å2
Refinement stepCycle: LAST / Resolution: 2.1→67.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 0 72 4601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624606
X-RAY DIFFRACTIONf_angle_d0.89396236
X-RAY DIFFRACTIONf_chiral_restr0.061739
X-RAY DIFFRACTIONf_plane_restr0.0043794
X-RAY DIFFRACTIONf_dihedral_angle_d24.08121677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.46381310.37623033X-RAY DIFFRACTION99.59
2.16-2.210.39711480.37482994X-RAY DIFFRACTION99.84
2.21-2.280.6041180.55992626X-RAY DIFFRACTION85.51
2.28-2.350.33021480.3293033X-RAY DIFFRACTION99.87
2.35-2.440.35311380.31473044X-RAY DIFFRACTION99.97
2.44-2.540.31941390.29793043X-RAY DIFFRACTION99.91
2.54-2.650.32751460.28843029X-RAY DIFFRACTION99.97
2.65-2.790.34011340.29293073X-RAY DIFFRACTION99.97
2.79-2.970.31541450.29013078X-RAY DIFFRACTION99.91
2.97-3.190.31450.28773054X-RAY DIFFRACTION99.81
3.19-3.520.32831420.25563084X-RAY DIFFRACTION99.97
3.52-4.020.26851490.22463097X-RAY DIFFRACTION99.69
4.02-5.070.20151500.19943137X-RAY DIFFRACTION99.85
5.07-67.410.23121540.23333270X-RAY DIFFRACTION99.8
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)
15.50663817907-1.91273697655-1.817663535552.477777939760.8904744084092.20678744436-0.767070466079-1.11431733257-0.4612564693830.4174501868740.575192511086-0.1513745361710.2842353117210.4595525832110.1996492343660.5156512085720.1609538307320.04408319723890.5170872334110.1082767596610.407986419763-9.00046413267-28.087372675415.200887592
28.723133878650.781985698793-2.293938576336.68920137104-0.2840635475925.62967446436-0.4807851137590.342925521588-0.159589758662-0.1117860320970.1703393643210.304205416877-0.0655266876316-0.4351656404940.3100488795010.4878560721150.02939244962540.08439253731910.379099656856-0.02105062787930.423203374838-3.24901273757-31.0966137822-2.03322071145
36.10601528491-1.44287414122-1.234007880472.70676478754-0.6695036965643.69546412955-0.749299414814-0.0832502085897-1.243118349740.0565745120480.4638598669490.1909216184590.78629289769-0.3666547545450.2357713763490.5890979159150.01816611924760.2783827925850.4627202936360.07867195534450.919833043508-13.0999798102-39.33204048677.64014053118
43.52036511213-0.00712834394482-1.176668075475.16254364576-1.482222373012.14695639548-0.3227933449021.33640711601-0.0825809756804-0.6950668709720.000172255956585-0.2018148743820.275947086658-0.6109238424230.3334383975220.620733811376-0.2249986801660.09731433448830.909575606206-0.03485279405490.516257435931-52.6266344099-55.035213158826.2470786059
56.1450852192-3.75638550711-2.209564438416.824099879884.780009359486.75663136426-0.2331458847771.30969416111-0.033204479466-0.595901806808-0.098606201947-0.5404975360710.000226037981127-0.5215183678080.3952872483430.727866774278-0.3941387849220.06195681415070.9106036470180.09151014133290.529313870057-55.3048060745-60.544314670327.3149576654
61.64935000747-0.597777601455-2.828364777472.65686413130.05631199442866.22138831744-0.3225842461742.24071914813-0.00919743909461-1.61990922373-0.249322753983-0.759712406927-0.282673885253-1.642116551330.5326627383671.26452280969-0.3214988554030.1645084892331.362027273760.3964914634310.683511424777-47.6934982064-50.332345779313.557266275
78.87006477687-4.71751425254-3.130552054633.384513060673.275857887863.50318234995-0.09696597097991.294913166350.257012755071-0.68687038121-0.600767380038-1.076442712070.7109842206940.1188994799740.5855693401481.59450643349-0.160516585580.3407190218511.232536765290.2365646933420.762340679221-43.8660889346-52.03426022067.22182319196
83.002847458741.607941107310.8764198311953.31157166292-0.648151604022.00984254110.09642253343310.9515585157650.130096630793-0.278320957368-0.428803975925-0.8876934828560.8494977550960.3083234707050.1880333608091.250498160870.0234664139430.5768679425780.9083990929280.3090938520321.36222162832-30.6449206901-54.288150812116.0715148224
94.277051292482.39245201283-2.390034906415.53025580464-1.954718670256.32310146079-0.1455545013680.8356830794970.459819435667-0.9706487042570.195924810256-0.6740206883040.248110166218-0.67277678599-0.008731821005460.834958735029-0.1654480984070.02983669313440.7559138446310.2901412195780.733011734697-45.0727239488-46.643042840820.1450870507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 188 )
2X-RAY DIFFRACTION2chain 'A' and (resid 189 through 265 )
3X-RAY DIFFRACTION3chain 'A' and (resid 266 through 336 )
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 70 )
5X-RAY DIFFRACTION5chain 'B' and (resid 71 through 110 )
6X-RAY DIFFRACTION6chain 'B' and (resid 111 through 151 )
7X-RAY DIFFRACTION7chain 'B' and (resid 152 through 228 )
8X-RAY DIFFRACTION8chain 'B' and (resid 229 through 298 )
9X-RAY DIFFRACTION9chain 'B' and (resid 299 through 335 )

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