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- PDB-2dre: Crystal structure of Water-soluble chlorophyll protein from lepid... -

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Basic information

Entry
Database: PDB / ID: 2dre
TitleCrystal structure of Water-soluble chlorophyll protein from lepidium virginicum at 2.00 angstrom resolution
ComponentsWater-soluble chlorophyll protein
KeywordsPLANT PROTEIN / BETA-TREFOIL / TETRAMER / PLANT / LEPIDIUM VIRGINICUM / CHLOROPHYLL / WATER-SOLUBLE CHLOROPHYLL PROTEIN / SINGLET OXYGEN / PHOTOOXIDATION / CHLOROPHYLL CARRIER / KUNITZ (STI) INHIBITORS
Function / homology
Function and homology information


endopeptidase inhibitor activity
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
CHLOROPHYLL A / Water-soluble chlorophyll protein
Similarity search - Component
Biological speciesLepidium virginicum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsHorigome, D. / Satoh, H. / Itoh, N. / Mitsunaga, K. / Oonishi, I. / Nakagawa, A. / Uchida, A.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Structural mechanism and photoprotective function of water-soluble chlorophyll-binding protein.
Authors: Horigome, D. / Satoh, H. / Itoh, N. / Mitsunaga, K. / Oonishi, I. / Nakagawa, A. / Uchida, A.
#1: Journal: Plant Cell.Physiol. / Year: 2001
Title: Water-soluble chlorophyll protein in Brassicaceae plants is a stress-induced chlorophyll-binding protein
Authors: Satoh, H. / Uchida, A. / Nakayama, K. / Okada, M.
#2: Journal: Biochim.Biophys.Acta / Year: 1980
Title: Crystallization of water-soluble chlorophyll-proteins from Lepidium virginicum
Authors: Murata, T. / Itoh, R. / Yakushiji, E.
History
DepositionJun 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Water-soluble chlorophyll protein
B: Water-soluble chlorophyll protein
C: Water-soluble chlorophyll protein
D: Water-soluble chlorophyll protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9408
Polymers78,3664
Non-polymers3,5744
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-98 kcal/mol
Surface area29830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.060, 82.730, 121.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Water-soluble chlorophyll protein


Mass: 19591.527 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-180 / Source method: isolated from a natural source / Source: (natural) Lepidium virginicum (plant) / Tissue: Leaf / References: UniProt: O04797
#2: Chemical
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M SODIUM/POTASSIUM PHOSPHATE, 3.2M AMMONIUM SULFATE, 5% SUCROSE, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2003
RadiationMonochromator: TRIANGULAR SI(111) WITH AN ASYMMETRIC ANGLE OF 7.8 DEGREES
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→28.99 Å / Num. obs: 50390 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.063 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.494 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 2→28.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1987876.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ALL OF THE FOUR CHLOROPHYLLS IN THE ASYMMETRIC UNIT WERE IDENTIFIED AS CHLOROPHYLL-A.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2489 4.9 %RANDOM
Rwork0.243 ---
obs0.243 50390 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.55 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.31 Å20 Å20 Å2
2--1.22 Å20 Å2
3---2.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5353 0 260 555 6168
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 389 4.7 %
Rwork0.319 7825 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CLA_CNS_PARAMCLA_CNS_TOP

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