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- PDB-1xmb: X-ray structure of IAA-aminoacid hydrolase from Arabidopsis thali... -

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Basic information

Entry
Database: PDB / ID: 1xmb
TitleX-ray structure of IAA-aminoacid hydrolase from Arabidopsis thaliana gene AT5G56660
ComponentsIAA-amino acid hydrolase homolog 2
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / AT5G56660 / ILL2 / indole-3-acetic acid / auxin / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


IAA-amino acid conjugate hydrolase activity / IAA-Ala conjugate hydrolase activity / auxin metabolic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / endoplasmic reticulum lumen / endoplasmic reticulum / metal ion binding
Similarity search - Function
IAA-amino acid hydrolase ILR1-like / Amidohydrolase / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Endoplasmic reticulum targeting sequence. / Zn peptidases ...IAA-amino acid hydrolase ILR1-like / Amidohydrolase / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Endoplasmic reticulum targeting sequence. / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IAA-amino acid hydrolase ILR1-like 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2009
Title: X-ray structure of ILL2, an auxin-conjugate amidohydrolase from Arabidopsis thaliana.
Authors: Bitto, E. / Bingman, C.A. / Bittova, L. / Houston, N.L. / Boston, R.S. / Fox, B.G. / Phillips Jr., G.N.
History
DepositionOct 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2013Group: Database references / Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IAA-amino acid hydrolase homolog 2


Theoretical massNumber of molelcules
Total (without water)45,5681
Polymers45,5681
Non-polymers00
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.264, 75.264, 130.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein IAA-amino acid hydrolase homolog 2


Mass: 45567.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ILL2 / Plasmid: pVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) p(LacI+RARE) / References: UniProt: P54970
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10 mg/mL PROTEIN, 0.080 M MAGNESIUM SULFATE, 14 % PEG 1500, 0.100 M CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.96411
SYNCHROTRONAPS 19-BM20.97932
Detector
TypeIDDetectorDateDetails
APS-11CCDAug 1, 2004Rosenbaum-Rock vertical focusing mirror
APS-12CCDJul 30, 2004Rosenbaum-Rock vertical focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock double-crystal monochromator: water cooled, sagitally focusing 2nd crystalSINGLE WAVELENGTHMx-ray1
2Rosenbaum-Rock double-crystal monochromator: water cooled, sagitally focusing 2nd crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.964111
20.979321
ReflectionResolution: 2→24.21 Å / Num. obs: 29672 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.043 / Χ2: 0.432 / Net I/σ(I): 22
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allΧ2% possible all
2-2.076.30.3343.829390.49199.9
2.07-2.150.21229070.348100
2.15-2.250.15829350.371100
2.25-2.370.1229250.379100
2.37-2.520.09529400.391100
2.52-2.710.06929450.401100
2.71-2.990.0529530.419100
2.99-3.420.03529860.45100
3.42-4.310.02730100.511100
4.31-500.02431320.57598.8

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.001 Å / D res low: 15 Å / FOM : 0.35 / Reflection: 28286
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
144.2869.77211.437SE20.10.56
240.52926.8436.218SE16.70.54
337.35428.70511.632SE26.80.62
446.41930.5252.999SE26.80.53
557.92928.8188.217SE28.10.68
646.71216.03615.583SE38.80.71
70.40436.1310.847SE20.60.4
8-15.65455.46111.185SE42.30.51
9-17.76749.5670.78SE46.70.52
Phasing MAD shell
Resolution (Å)FOM Reflection
6.75-150.451608
4.42-6.750.412512
3.5-4.420.443132
2.99-3.50.463590
2.65-2.990.414013
2.4-2.650.354311
2.21-2.40.254507
2.06-2.210.184613
Phasing dmFOM : 0.64 / FOM acentric: 0.64 / FOM centric: 0.61 / Reflection: 28287 / Reflection acentric: 25455 / Reflection centric: 2832
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-14.9840.930.930.811302969333
3.6-5.70.910.930.8240343423611
2.9-3.60.820.840.6849284387541
2.5-2.90.690.70.5548954446449
2.1-2.50.520.530.4582857680605
2-2.10.320.330.2748434550293

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
ARP/wARP2.06model building
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
RefinementMethod to determine structure: SAD / Resolution: 2→24.21 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.153 / SU B: 3.155 / SU ML: 0.09 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.14 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 1504 5.076 %RANDOM
Rwork0.1567 ---
all0.159 ---
obs0.159 29630 99.821 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 27.747 Å2
Baniso -1Baniso -2Baniso -3
1--0.005 Å2-0.003 Å20 Å2
2---0.005 Å20 Å2
3---0.008 Å2
Refinement stepCycle: LAST / Resolution: 2→24.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 0 0 285 3174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222954
X-RAY DIFFRACTIONr_bond_other_d0.0010.022738
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.9643993
X-RAY DIFFRACTIONr_angle_other_deg0.83836384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50324.113124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35515516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7471516
X-RAY DIFFRACTIONr_chiral_restr0.0990.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023259
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02571
X-RAY DIFFRACTIONr_nbd_refined0.2090.2604
X-RAY DIFFRACTIONr_nbd_other0.1890.22665
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21442
X-RAY DIFFRACTIONr_nbtor_other0.0880.21687
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.2222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.218
X-RAY DIFFRACTIONr_mcbond_it2.19322385
X-RAY DIFFRACTIONr_mcbond_other0.3532764
X-RAY DIFFRACTIONr_mcangle_it2.87242997
X-RAY DIFFRACTIONr_mcangle_other1.33942563
X-RAY DIFFRACTIONr_scbond_it5.45461249
X-RAY DIFFRACTIONr_scbond_other1.82862316
X-RAY DIFFRACTIONr_scangle_it7.0818996
X-RAY DIFFRACTIONr_scangle_other3.06583821
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0520.2471100.1862058218199.404
2.052-2.1080.251970.16819842081100
2.108-2.1690.21150.16219422057100
2.169-2.2360.2191050.1618721977100
2.236-2.3090.192960.15418341930100
2.309-2.390.2081150.15817601875100
2.39-2.480.2011040.15617081812100
2.48-2.5810.161850.15716531738100
2.581-2.6960.216880.16315981686100
2.696-2.8270.268750.16415191594100
2.827-2.980.218740.16114711545100
2.98-3.160.241690.15413751444100
3.16-3.3780.223660.14912971363100
3.378-3.6480.208630.14612141277100
3.648-3.9950.193570.13611391196100
3.995-4.4640.152510.13510211072100
4.464-5.1510.166440.14491495999.896
5.151-6.2990.183440.181791835100
6.299-8.8660.213310.189627658100
8.866-65.2330.219150.19234940390.323

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