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- PDB-2hcz: Crystal structure of EXPB1 (Zea m 1), a beta-expansin and group-1... -

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Basic information

Entry
Database: PDB / ID: 2hcz
TitleCrystal structure of EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize
ComponentsBeta-expansin 1a
KeywordsALLERGEN / Domain 1 is a beta barrel and Domain 2 is a immunoglobulin like beta-sandwich
Function / homology
Function and homology information


sexual reproduction / cell wall / cell wall organization / extracellular region / membrane
Similarity search - Function
Major pollen allergen Lol pI / Expansin/Lol pI / Rare lipoprotein A (RlpA)-like double-psi beta-barrel / Expansin, Cellulose-binding-like domain profile. / Expansin, cellulose-binding-like domain / Expansin C-terminal domain / Expansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / Expansin, cellulose-binding-like domain / RlpA-like protein, double-psi beta-barrel domain ...Major pollen allergen Lol pI / Expansin/Lol pI / Rare lipoprotein A (RlpA)-like double-psi beta-barrel / Expansin, Cellulose-binding-like domain profile. / Expansin, cellulose-binding-like domain / Expansin C-terminal domain / Expansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / Expansin, cellulose-binding-like domain / RlpA-like protein, double-psi beta-barrel domain / Expansin, cellulose-binding-like domain superfamily / Lytic transglycolase / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsYennawar, N.H. / Cosgrove, D.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structure and activities of EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize.
Authors: Yennawar, N.H. / Li, L.C. / Dudzinski, D.M. / Tabuchi, A. / Cosgrove, D.J.
History
DepositionJun 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
X: Beta-expansin 1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1232
Polymers26,9341
Non-polymers1,1891
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.408, 44.512, 69.467
Angle α, β, γ (deg.)90.000, 124.640, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-expansin 1a / Pollen allergen Zea m 1 / Zea m I


Mass: 26934.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / Tissue: pollen / References: UniProt: P58738
#2: Polysaccharide alpha-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1189.079 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-2[DManpa1-3][DManpa1-6]DManpa1-4DGlcpNAcb1-4[DFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a2112m-1a_1-5][a1122h-1a_1-5][a212h-1a_1-5]/1-2-1-3-4-3-3/a3-b1_a4-c1_c4-d1_d2-e1_d3-f1_d6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(2+1)][a-D-Xylp]{}[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15% PEG 4000, 50mM Sodium Acetate and 0.1M Ammonium Sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 1998 / Details: Graphite
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→100 Å / Num. all: 7531 / Num. obs: 7013 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.079 / Χ2: 0.958 / Net I/σ(I): 7.3
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.402 / Num. unique all: 705 / Χ2: 0.212 / % possible all: 96.6

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Phasing

Phasing MRRfactor: 0.514 / Cor.coef. Fo:Fc: 0.478 / Cor.coef. Io to Ic: 0.263
Highest resolutionLowest resolution
Rotation2.75 Å56.796 Å
Translation2.75 Å56.796 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 6886
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.45-10046.50.734503
5.08-6.4545.20.747501
4.47-5.0837.40.807503
4.09-4.4734.40.832507
3.81-4.0937.90.796501
3.6-3.8131.30.827502
3.43-3.634.10.822503
3.29-3.4338.90.816501
3.16-3.2937.90.8504
3.06-3.1637.60.775507
2.96-3.0640.20.761504
2.88-2.9647.30.768509
2.75-2.8847.50.745841

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
DM4.1phasing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N10

1n10


Resolution: 2.75→29.63 Å / FOM work R set: 0.699 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 367 4.8 %RANDOM
Rwork0.233 ---
all0.233 7531 --
obs0.233 7007 92.1 %-
Solvent computationBsol: 46.183 Å2
Displacement parametersBiso mean: 56.865 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å2-1.449 Å2
2---4.798 Å20 Å2
3---6.439 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 80 17 1969
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.65
X-RAY DIFFRACTIONc_bond_d0.008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.75-2.870.545410.42780821
2.87-3.030.378500.368860910
3.03-3.220.397470.331850897
3.22-3.460.33560.262836892
3.46-3.810.322400.213860900
3.81-4.360.245390.216856895
4.36-5.480.205550.16779834
5.48-250.274380.192813851
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2carbohydrate.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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