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- PDB-9lh0: High-resolution crystal structure of an isoform of Chitin Binding... -

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Basic information

Entry
Database: PDB / ID: 9lh0
TitleHigh-resolution crystal structure of an isoform of Chitin Binding Protein from Iberis umbellata L.
Components(Chitin Binding ...) x 2
KeywordsPLANT PROTEIN / Isoform / Chitin Binding Protein / Iberis / Candytuft
Function / homologyACETIC ACID / : / NITRATE ION
Function and homology information
Biological speciesIberis umbellata (globe candytuft)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.91 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 Chitin Binding Protein from Iberis umbellata L.
Authors: Saeed, A. / Betzel, C. / Brognaro, H. / Rajaiah Prabhu, P. / Alves Franca, B. / Mehmood, S. / Ishaq, U. / Khaliq, B. / Akrem, A.
History
DepositionJan 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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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)12,47710
Polymers11,9742
Non-polymers5038
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-42 kcal/mol
Surface area6840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.352, 72.981, 31.373
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 ... , 2 types, 2 molecules AB

#1: Protein/peptide Chitin Binding Protein


Mass: 3757.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Iberis umbellata (globe candytuft)
#2: Protein Chitin Binding Protein


Mass: 8216.560 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, 42 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-LI / LITHIUM ION


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


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 43.86 %
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: 0.6888 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: 0.6888 Å / Relative weight: 1
ReflectionResolution: 0.91→28.82 Å / Num. obs: 76151 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 11.64 Å2 / CC1/2: 0.99 / CC star: 0.99 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.026 / Rrim(I) all: 0.06 / Net I/av σ(I): 9.39 / Net I/σ(I): 9.39
Reflection shellResolution: 0.91→0.92 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 9.39 / Num. unique obs: 555 / CC1/2: 0.012 / CC star: 0.16 / Rpim(I) all: 0.019 / Rrim(I) all: 0.06 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.91→28.82 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1861 3828 5.03 %
Rwork0.1763 --
obs0.1768 76084 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.91→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 31 34 898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.763
X-RAY DIFFRACTIONf_dihedral_angle_d13.975335
X-RAY DIFFRACTIONf_chiral_restr0.084129
X-RAY DIFFRACTIONf_plane_restr0.01163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.91-0.920.27911420.24682619X-RAY DIFFRACTION99
0.92-0.930.23911340.22632638X-RAY DIFFRACTION100
0.93-0.940.22171540.2082638X-RAY DIFFRACTION100
0.94-0.960.20161510.19092623X-RAY DIFFRACTION100
0.96-0.970.22011340.17882630X-RAY DIFFRACTION100
0.97-0.990.17971200.17442696X-RAY DIFFRACTION100
0.99-10.18041370.16762632X-RAY DIFFRACTION100
1-1.020.15821340.15032658X-RAY DIFFRACTION100
1.02-1.040.15221280.14812632X-RAY DIFFRACTION100
1.04-1.060.16951440.14632677X-RAY DIFFRACTION100
1.06-1.080.17031440.15282646X-RAY DIFFRACTION100
1.08-1.10.17741450.15122646X-RAY DIFFRACTION100
1.1-1.130.12481482655X-RAY DIFFRACTION100
1.13-1.160.14831550.13462652X-RAY DIFFRACTION100
1.16-1.190.13531490.13532638X-RAY DIFFRACTION100
1.19-1.220.16851480.13982659X-RAY DIFFRACTION100
1.22-1.260.13691472663X-RAY DIFFRACTION100
1.26-1.310.14931360.13962684X-RAY DIFFRACTION100
1.31-1.360.14971400.1452662X-RAY DIFFRACTION100
1.36-1.420.13871420.13842686X-RAY DIFFRACTION100
1.42-1.50.15781260.14892722X-RAY DIFFRACTION100
1.5-1.590.17951330.14922689X-RAY DIFFRACTION100
1.59-1.710.18321280.15692720X-RAY DIFFRACTION100
1.71-1.890.21271530.17922715X-RAY DIFFRACTION100
1.89-2.160.21231320.18392738X-RAY DIFFRACTION100
2.16-2.720.20841540.19522763X-RAY DIFFRACTION100
2.72-8.80.19141702875X-RAY DIFFRACTION99

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