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- PDB-9v6z: Crystal structure of Isoform Chitin Binding Protein from Iberis u... -

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Basic information

Entry
Database: PDB / ID: 9v6z
TitleCrystal structure of Isoform Chitin Binding Protein from Iberis umbellata L.
Components(Chitin Binding Protein ...) x 2
KeywordsPLANT PROTEIN / Isoform / Chitin Binding Protein / Iberis / Candytuft
Function / homologyACETATE ION / NITRATE ION
Function and homology information
Biological speciesIberis umbellata (globe candytuft)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsSaeed, A. / Betzel, C. / Brognaro, H. / Rajaiah Prabhu, P. / Alves Franca, B. / Mehmood, S. / Khaliq, B. / Ishaq, U. / Akrem, A.
Funding support Pakistan, 1items
OrganizationGrant numberCountry
Other governmentIRSIP Pakistan
CitationJournal: To Be Published
Title: Crystal structure of Isoform Chitin Binding Protein from Iberis umbellata L.
Authors: Saeed, A. / Betzel, C. / Brognaro, H. / Rajaiah Prabhu, P. / Alves Franca, B. / Mehmood, S. / Khaliq, B. / Ishaq, U. / Akrem, A.
History
DepositionMay 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,28713
Polymers11,7392
Non-polymers54811
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.179, 73.121, 31.296
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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

#1: Protein/peptide Chitin Binding Protein III


Mass: 3661.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Iberis umbellata (globe candytuft)
#2: Protein Chitin Binding Protein III


Mass: 8078.433 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, 63 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3O2 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 2.2M Ammonium sulfate, 0.2M Lithium 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: P13 (MX1) / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2024
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.4→31.2 Å / Num. obs: 19586 / % possible obs: 100 % / Redundancy: 5.3 % / Biso Wilson estimate: 17.8239 Å2 / CC1/2: 0.998 / CC star: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 / Net I/σ(I): 0.3
Reflection shellResolution: 1.44→1.51 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 5.55 / Num. unique obs: 3620 / CC1/2: 0.0003 / CC star: 0.0246 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→28.42 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 963 4.92 %
Rwork0.1897 --
obs0.191 19582 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms817 0 28 52 897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006854
X-RAY DIFFRACTIONf_angle_d0.7791155
X-RAY DIFFRACTIONf_dihedral_angle_d12.587312
X-RAY DIFFRACTIONf_chiral_restr0.076125
X-RAY DIFFRACTIONf_plane_restr0.009153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.510.2821470.24612595X-RAY DIFFRACTION100
1.51-1.610.22321410.19982609X-RAY DIFFRACTION100
1.61-1.730.19231460.18912607X-RAY DIFFRACTION100
1.73-1.90.26991250.18732632X-RAY DIFFRACTION100
1.9-2.180.18491340.18282648X-RAY DIFFRACTION100
2.18-2.750.22611370.19612699X-RAY DIFFRACTION100
2.75-3.090.21621330.18442829X-RAY DIFFRACTION100

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