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- PDB-4m9w: Crystal Structure of Ara h 8 with MES bound -

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Basic information

Entry
Database: PDB / ID: 4m9w
TitleCrystal Structure of Ara h 8 with MES bound
ComponentsAra h 8 allergen
KeywordsPLANT PROTEIN / Bet v 1 like / Small Molecule Carrier
Function / homology
Function and homology information


response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Pathogenesis-related proteins Bet v I family signature. / 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
Biological speciesArachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsOffermann, L.R. / Hurlburt, B.K. / Majorek, K.A. / McBride, J.K. / Maleki, S.J. / Chruszcz, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure and Function of the Peanut Panallergen Ara h 8.
Authors: Hurlburt, B.K. / Offermann, L.R. / McBride, J.K. / Majorek, K.A. / Maleki, S.J. / Chruszcz, M.
History
DepositionAug 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Sep 20, 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_ncs_dom_lim / 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_asym_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_asym_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_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Assembly

Deposited unit
A: Ara h 8 allergen
B: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1885
Polymers33,9462
Non-polymers2413
Water2,468137
1
A: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9962
Polymers16,9731
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ara h 8 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1913
Polymers16,9731
Non-polymers2182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.183, 87.488, 42.290
Angle α, β, γ (deg.)90.00, 95.84, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 2 - 157 / Label seq-ID: 2 - 157

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ara h 8 allergen


Mass: 16973.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Plasmid: pET-A8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6VT83
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES (6.5), 25% PEG 2000MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2012
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 21429 / Num. obs: 21429 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 35.9
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1081 / Rsym value: 0.364 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 4M9B

4m9b


Resolution: 1.95→40.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.561 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.203 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24796 1092 5.1 %RANDOM
Rwork0.2054 ---
all0.20758 20162 --
obs0.20758 20162 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.889 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å2-0 Å2-2.62 Å2
2---4 Å2-0 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 14 137 2508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022419
X-RAY DIFFRACTIONr_bond_other_d0.0050.022339
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9983278
X-RAY DIFFRACTIONr_angle_other_deg1.23435450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5565312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80226.52292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65915422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.14152
X-RAY DIFFRACTIONr_chiral_restr0.1050.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212691
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02451
Refine LS restraints NCS

Ens-ID: 1 / Number: 7910 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 83 -
Rwork0.286 1492 -
obs--99.75 %
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)
11.5339-0.24181.31882.4393-0.69981.8370.05570.1136-0.08060.1174-0.0385-0.17170.07290.0461-0.01720.09260.00830.07790.207-0.01030.120313.5120.0944.6889
20.91630.26331.14872.53360.7131.95050.0368-0.0383-0.02780.15650.0651-0.1007-0.053-0.0784-0.1020.09990.0040.07520.18830.0160.0934.5687-25.50216.12
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 13
2X-RAY DIFFRACTION1A14 - 36
3X-RAY DIFFRACTION1A37 - 76
4X-RAY DIFFRACTION1A77 - 123
5X-RAY DIFFRACTION1A124 - 157
6X-RAY DIFFRACTION2B2 - 13
7X-RAY DIFFRACTION2B14 - 36
8X-RAY DIFFRACTION2B37 - 76
9X-RAY DIFFRACTION2B77 - 123
10X-RAY DIFFRACTION2B124 - 157

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