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- PDB-1xdf: Crystal structure of pathogenesis-related protein LlPR-10.2A from... -

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Basic information

Entry
Database: PDB / ID: 1xdf
TitleCrystal structure of pathogenesis-related protein LlPR-10.2A from yellow lupine
ComponentsPR10.2A
KeywordsPLANT PROTEIN / 7-stranded antiparallel beta-sheet / kinked C-terminal alpha-helix / glycine-rich loop
Function / homology
Function and homology information


cytokinin binding / melatonin binding / abscisic acid binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / RNA nuclease activity / defense response / signaling receptor activity / calcium ion binding ...cytokinin binding / melatonin binding / abscisic acid binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / RNA nuclease activity / defense response / signaling receptor activity / calcium ion binding / nucleus / cytosol
Similarity search - Function
Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Class 10 plant pathogenesis-related protein 2A
Similarity search - Component
Biological speciesLupinus luteus (yellow lupine)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPasternak, O. / Biesiadka, J. / Dolot, R. / Handschuh, L. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclass.
Authors: Pasternak, O. / Biesiadka, J. / Dolot, R. / Handschuh, L. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structures of two homologous pathogenesis-related proteins from yellow lupine
Authors: Biesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
#2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1999
Title: Crystallization and preliminary x-ray structure determination of Lupinus luteus PR10 protein
Authors: Biesiadka, J. / Sikorski, M.M. / Bujacz, G. / Jaskolski, M.
#3: Journal: Nat.Struct.Biol. / Year: 1996
Title: X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy
Authors: Gajhede, M. / Osmark, P. / Poulsen, F.M. / Ipsen, H. / Larsen, J.N. / van Neerven, R.J.J. / Schou, C. / Lowenstein, H. / Spangfort, M.D.
#4: Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of a hypoallergenic isoform of the major birch pollen allergen Bet v 1 and its likely biological function as a plant steroid carrier
Authors: Markovic-Housley, Z. / Degano, M. / Lamba, D. / von Roepenack-Lahaye, E. / Clemens, S. / Susani, M. / Ferreira, F. / Scheiner, O. / Breiteneder, H.
History
DepositionSep 6, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PR10.2A
B: PR10.2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8474
Polymers33,5862
Non-polymers2612
Water5,062281
1
A: PR10.2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0543
Polymers16,7931
Non-polymers2612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PR10.2A


Theoretical massNumber of molelcules
Total (without water)16,7931
Polymers16,7931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.956, 69.243, 112.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. THE PROTEIN IS MONOMERIC AND THE TWO CHAINS, A AND B, ARE NOT INVOLVED IN QUATERNARY STRUCTURE FORMATION.

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Components

#1: Protein PR10.2A / LlPR-10.2A


Mass: 16792.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lupinus luteus (yellow lupine) / Gene: Llpr-10.2a / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9LLQ3
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.71 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium citrate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 10, 2000 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 30830 / Num. obs: 30830 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 28.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3000 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IFV

1ifv


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.413 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: H ATOMS AT RIDING POSITIONS WERE INCLUDED IN FC CALCULATIONS; ONE OF THE TWO PROTEIN MOLECULES COORDINATES A SODIUM CATION; THE REFINEMENT INCLUDED TLS PARAMETERS; THE TIPS OF 6 SURFACE ...Details: H ATOMS AT RIDING POSITIONS WERE INCLUDED IN FC CALCULATIONS; ONE OF THE TWO PROTEIN MOLECULES COORDINATES A SODIUM CATION; THE REFINEMENT INCLUDED TLS PARAMETERS; THE TIPS OF 6 SURFACE RESIDUES (1 IN MOL. A, 5 IN MOL. B) HAVE NOT BEEN MEDELED BECAUSE OF MISSING ELECTRON DENSITY, AND THE CORRESPONDING ATOMS ARE NOT INCLUDED IN THE MODEL (SEE REMARK 470);
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1193 4 %RANDOM
Rwork0.205 ---
all0.207 28579 --
obs0.207 28579 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.01 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--3.13 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 16 281 2643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212397
X-RAY DIFFRACTIONr_bond_other_d0.0020.022195
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.983239
X-RAY DIFFRACTIONr_angle_other_deg0.92635143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3335312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022676
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02430
X-RAY DIFFRACTIONr_nbd_refined0.2220.2447
X-RAY DIFFRACTIONr_nbd_other0.2510.22484
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.21458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2174
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.77911548
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.01322475
X-RAY DIFFRACTIONr_scbond_it4.4233849
X-RAY DIFFRACTIONr_scangle_it6.233764
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.343 73
Rwork0.298 1879
obs-2193
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)
12.77770.2806-0.10572.23360.73252.46120.1609-0.174-0.0604-0.0968-0.0664-0.1641-0.0070.1104-0.09450.11610.01270.01850.0490.04740.067814.50896.883113.215
22.5619-0.70070.60432.80050.54783.36620.0011-0.02740.5174-0.1269-0.0004-0.3532-0.33420.0365-0.00080.07350.02760.03570.035-0.04230.143414.532339.955818.2491
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1571 - 157
2X-RAY DIFFRACTION2BB1 - 1571 - 157

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