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- PDB-9gvh: Crystal structure of Chitin Binding Protein from Iberis umbellata L. -

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Basic information

Entry
Database: PDB / ID: 9gvh
TitleCrystal structure of Chitin Binding Protein from Iberis umbellata L.
Components(Chitin Binding ...) x 2
KeywordsPLANT PROTEIN / Chitin Binding Protein / 2S Albumin / Plant Lipid Transfer protein / Seed Storage Helical Domain-Containing protein.
Function / homologyACETATE ION / NITRATE ION
Function and homology information
Biological speciesIberis umbellata (globe candytuft)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsSaeed, A. / Betzel, C. / Brognaro, H. / Alves Franca, B. / Mehmood, S. / Rajaiah Prabhu, P. / Ishaq, U. / Akrem, A.
Funding support Pakistan, 1items
OrganizationGrant numberCountry
Other governmentIRSIP 51 BMS 32 Pakistan
CitationJournal: To be published
Title: Crystal structure of Chitin Binding Protein from Iberis umbellata L.
Authors: Saeed, A. / Betzel, C. / Brognaro, H. / Alves Franca, B. / Mehmood, S. / Rajaiah Prabhu, P. / Ishaq, U. / Akrem, A.
History
DepositionSep 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Revision 2.0Jul 16, 2025Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / cell / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_rmsd_angle / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_ref_seq / symmetry
Item: _cell.volume / _chem_comp.formula ..._cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.pdbx_end_seq_num / _pdbx_modification_feature.auth_seq_id / _pdbx_modification_feature.label_seq_id / _pdbx_modification_feature.modified_residue_auth_seq_id / _pdbx_modification_feature.modified_residue_label_seq_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _software.version / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _symmetry.space_group_name_Hall
Description: Sequence discrepancy
Details: 1. The amino acid sequence numbering has been updated. In the previous PDB file (9GVH), the sequence started at position -1. In the updated version, it starts at position 1 to match the ...Details: 1. The amino acid sequence numbering has been updated. In the previous PDB file (9GVH), the sequence started at position -1. In the updated version, it starts at position 1 to match the canonical sequence numbering. 2. The following residue sequence changes were made to correct discrepancies: Pro -1 to Ala 1 Lys 27 to Ser 29 Val 30 to Thr 32 Gly 56 to Gln 55 Gly 57 to Gln 56 Glu 58 to Arg 57 Val 78 to Thr 76 Met 80 to Ser 80 Gln 87 to Met 85 Val 79 to Thr 87 Ser 90 to Ser 88 Ser 96 to Gln 94 Ser 98 to Ala 96 Asn 116 to Ser 114 Thr 126 to Val 124 These modifications align the structure with the correct reference sequence and ensure accurate residue annotation.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitin Binding Protein
B: Chitin Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,84519
Polymers11,8472
Non-polymers99817
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.135, 73.235, 31.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Chitin Binding ... , 2 types, 2 molecules AB

#1: Protein/peptide Chitin Binding Protein


Mass: 3658.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Iberis umbellata (globe candytuft)
#2: Protein Chitin Binding Protein


Mass: 8188.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Iberis umbellata (globe candytuft)

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Non-polymers , 6 types, 69 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 2.2M Ammonium sulfate, 0.2M Sodium Nitrate or Ammonium nitrate/Lithium nitrate/Potasium nitrate 16-20mg Protein in 50mM Sodium acetate, 150mM Sodium Chloride, pH 4.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97621 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jul 22, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97621 Å / Relative weight: 1
ReflectionResolution: 1.34→28.74 Å / Num. obs: 23901 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 12.97 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.06 / Rrim(I) all: 0.15 / Net I/av σ(I): 4.25 / Net I/σ(I): 4.25
Reflection shellResolution: 1.34→1.4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 4.25 / Num. unique obs: 3379 / CC1/2: 0.03 / CC star: 0.25 / Rpim(I) all: 0.034 / Rrim(I) all: 0.12 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
autoPROCdata processing
pointlessdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→28.74 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 1184 4.95 %
Rwork0.1895 --
obs0.1906 23896 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.34→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms824 0 59 52 935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007885
X-RAY DIFFRACTIONf_angle_d0.8421194
X-RAY DIFFRACTIONf_dihedral_angle_d14.039311
X-RAY DIFFRACTIONf_chiral_restr0.083130
X-RAY DIFFRACTIONf_plane_restr0.01162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.40.22481530.23092780X-RAY DIFFRACTION100
1.4-1.480.2191600.20152783X-RAY DIFFRACTION100
1.48-1.570.23171420.1762805X-RAY DIFFRACTION100
1.57-1.690.20491290.17822811X-RAY DIFFRACTION100
1.69-1.860.20051390.18432815X-RAY DIFFRACTION100
1.86-2.130.20551480.18152841X-RAY DIFFRACTION100
2.13-2.680.24261560.18842863X-RAY DIFFRACTION100
2.68-28.740.19631570.19293014X-RAY DIFFRACTION100

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