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- PDB-1nar: CRYSTAL STRUCTURE OF NARBONIN REFINED AT 1.8 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1nar
TitleCRYSTAL STRUCTURE OF NARBONIN REFINED AT 1.8 ANGSTROMS RESOLUTION
ComponentsNARBONIN
KeywordsPLANT SEED PROTEIN
Function / homology
Function and homology information


carbohydrate metabolic process
Similarity search - Function
Chitinase-like / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesVicia narbonensis (plant)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsHennig, M. / Schlesier, B. / Wilson, K.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Crystal structure of narbonin at 1.8 A resolution.
Authors: Hennig, M. / Pfeffer-Hennig, S. / Dauter, Z. / Wilson, K.S. / Schlesier, B. / Nong, V.H.
#1: Journal: FEBS Lett. / Year: 1992
Title: A Tim Barrel Protein without Enzymatic Activity? Crystal Structure of Narbonin at 1.8 Angstroms Resolution
Authors: Hennig, M. / Schlesier, B. / Dauter, Z. / Pfeffer, S. / Betzel, C. / Hoehne, W.E. / Wilson, K.S.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Narbonin, a 2S Globulin from Vicia Narbonensis L. Crystallization and Preliminary Crystallographic Data
Authors: Hennig, M. / Schlesier, B. / Pfeffer, S. / Hoehne, W.E.
History
DepositionSep 10, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET THE SHEET PRESENTED AS *A* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *A* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NARBONIN


Theoretical massNumber of molelcules
Total (without water)33,1401
Polymers33,1401
Non-polymers00
Water9,242513
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.900, 75.500, 50.900
Angle α, β, γ (deg.)90.00, 120.50, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: GLY 38 - PHE 39 OMEGA = 9.34 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO 139
3: TRP 261 - ASN 262 OMEGA = 12.67 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein NARBONIN


Mass: 33140.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicia narbonensis (plant) / References: UniProt: Q08884
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AMINO ACID SEQUENCE WAS DETERMINED BY INTERPRETATION OF THE ELECTRON DENSITY (REF. 1). FOR ...THE AMINO ACID SEQUENCE WAS DETERMINED BY INTERPRETATION OF THE ELECTRON DENSITY (REF. 1). FOR FINAL REFINEMENT THE SEQUENCE WAS CORRECTED AT SEVERAL POSITIONS USING CDNA AND GENOMIC SEQUENCE: SEQUENCE ENTRIES XEMBL: VNNAF6NB, VNNAG2NB, VNNAN21NB.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal grow
*PLUS
pH: 9.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mg/mlprotein1drop
20.1 MTris-HCl1drop
30.45 M1dropNaCl
40.1 MTris-HCl1reservoir(pH 7.2)
5acetic acid1reservoirsome drops

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. obs: 27227 / % possible obs: 95.5 % / Num. measured all: 124224 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / Rmerge(I) obs: 0.078

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.159 27227
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 0 513 2846
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0460.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0880.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8351
X-RAY DIFFRACTIONp_mcangle_it1.4331.4
X-RAY DIFFRACTIONp_scbond_it2.2142.1
X-RAY DIFFRACTIONp_scangle_it3.3842.1
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1750.15
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.2680.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.230.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor17.543
X-RAY DIFFRACTIONp_staggered_tor16.9815
X-RAY DIFFRACTIONp_orthonormal_tor22.0120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. reflection all: 27227 / σ(F): 0 / Rfactor all: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21 Å2

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