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- PDB-1q9b: CRYSTAL STRUCTURE ANALYSIS OF Hev b 6.02 (HEVEIN) AT 1.5 ANGSTROM... -

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Basic information

Entry
Database: PDB / ID: 1q9b
TitleCRYSTAL STRUCTURE ANALYSIS OF Hev b 6.02 (HEVEIN) AT 1.5 ANGSTROMS RESOLUTION
ComponentsHevein
KeywordsALLERGEN / LECTIN / AGGLUTININ-TOXIN MOTIF
Function / homology
Function and homology information


chitin binding / RNA nuclease activity / defense response to fungus / defense response to bacterium
Similarity search - Function
Barwin domain / Barwin, conserved site / Pathogenesis-related protein-4 / Barwin family / Barwin domain signature 1. / Barwin domain signature 2. / Barwin domain profile. / Endochitinase-like / Chitin-binding, type 1, conserved site / Chitin recognition protein ...Barwin domain / Barwin, conserved site / Pathogenesis-related protein-4 / Barwin family / Barwin domain signature 1. / Barwin domain signature 2. / Barwin domain profile. / Endochitinase-like / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / RlpA-like domain superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRodriguez-Romero, A. / Hernandez-Santoyo, A.
Citation
#1: Journal: FEBS Lett. / Year: 1991
Title: Crystal Structure of Hevein at 2.8 A Resolution
Authors: Rodriguez-Romero, A. / Ravichandran, K.G. / Soriano-Garcia, M.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hevein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9683
Polymers4,7311
Non-polymers2362
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.810, 60.950, 22.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein/peptide Hevein / HEV b 6.02


Mass: 4731.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hevea brasiliensis (rubber tree) / Tissue: LATEX / References: UniProt: P02877
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: MPD, Tris-HCl, pH 7.10, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.1 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
160 %MPD1reservoir
240 mMTris-HCl1reservoirpH7.1

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1999
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.5→15 Å / Num. all: 7678 / Num. obs: 7332 / % possible obs: 95.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.9 Å2 / Rsym value: 0.05 / Net I/σ(I): 6.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 12.3 / Num. unique all: 635 / Rsym value: 0.046 / % possible all: 97.2
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 15 Å / Num. obs: 7113 / Redundancy: 4.7 % / Num. measured all: 57822 / Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
SHELXL-97refinement
SCALAdata scaling
Agrovatadata reduction
TRUNCATEdata reduction
CNSrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HEV

1hev


Resolution: 1.5→9.5 Å / Num. parameters: 3772 / Num. restraintsaints: 4884 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE ALTERNATE CONFORMATIONS EVENTUALLY REDUCED FREE R FROM 21.19-19.20%. INTRODUCTION OF ANISOTROPIC REFINEMENT REDUCED FREE R FROM 19.20- 16.01%. DISCRETELY DISORDERED HETEROGENS: 2, MPD ...Details: THE ALTERNATE CONFORMATIONS EVENTUALLY REDUCED FREE R FROM 21.19-19.20%. INTRODUCTION OF ANISOTROPIC REFINEMENT REDUCED FREE R FROM 19.20- 16.01%. DISCRETELY DISORDERED HETEROGENS: 2, MPD 101 AND MPD 102; DISCRETELY DISORDERED RESIDUES: 6, GLU 1, LEU 11, PRO 13, SER 26, GLU 29, PRO 33. ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.145 698 10 %RANDOM
all0.128 6996 --
obs0.128 6980 94.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 268 / Occupancy sum non hydrogen: 379
Refinement stepCycle: LAST / Resolution: 1.5→9.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms345 0 32 39 416
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0214
X-RAY DIFFRACTIONs_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.034
X-RAY DIFFRACTIONs_approx_iso_adps0.065
LS refinement shellResolution: 1.5→1.53 Å / Num. reflection Rfree: 63 / Num. reflection obs: 635
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.128
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_plane_restr0.021
X-RAY DIFFRACTIONs_chiral_restr0.06

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