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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 / homologyACETIC ACID / : / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,79015
Polymers11,9432
Non-polymers84713
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-52 kcal/mol
Surface area6630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.135, 73.235, 31.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
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
Components on special symmetry positions
IDModelComponents
11B-332-

HOH

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Components

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

#1: Protein/peptide Chitin Binding Protein


Mass: 3740.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Iberis umbellata (globe candytuft)
#2: Protein Chitin Binding Protein


Mass: 8202.554 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Iberis umbellata (globe candytuft)

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Non-polymers , 5 types, 69 molecules

#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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
PHENIX1.21.2_5419refinement
autoPROCdata processing
pointlessdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→28.74 Å / SU ML: 0.1331 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.6753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1936 1184 4.95 %
Rwork0.1555 22713 -
obs0.1573 23897 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.18 Å2
Refinement stepCycle: LAST / Resolution: 1.34→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms831 0 52 56 939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138899
X-RAY DIFFRACTIONf_angle_d1.25181213
X-RAY DIFFRACTIONf_chiral_restr0.1005130
X-RAY DIFFRACTIONf_plane_restr0.015164
X-RAY DIFFRACTIONf_dihedral_angle_d12.7932322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.40.24881530.19122780X-RAY DIFFRACTION99.9
1.4-1.480.20441600.14962784X-RAY DIFFRACTION99.9
1.48-1.570.2111420.13162805X-RAY DIFFRACTION99.9
1.57-1.690.19381290.13292811X-RAY DIFFRACTION99.97
1.69-1.860.17251390.13142815X-RAY DIFFRACTION99.8
1.86-2.130.1831480.13512841X-RAY DIFFRACTION99.93
2.13-2.680.21071560.15482863X-RAY DIFFRACTION100
2.68-28.740.18291570.17423014X-RAY DIFFRACTION99.81

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