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- PDB-4pmk: Crystal structure of kiwellin -

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Basic information

Entry
Database: PDB / ID: 4pmk
TitleCrystal structure of kiwellin
ComponentsKiwellin
KeywordsPLANT PROTEIN / double psi beta barrel
Function / homologyKiwellin-like / RlpA-like domain superfamily / extracellular region / Kiwellin / Kiwellin
Function and homology information
Biological speciesActinidia chinensis (golden kiwifruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsHamiaux, C. / Baker, E.N. / Atkinson, R.G.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
MBIE New Zealand
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Crystal structure of kiwellin, a major cell-wall protein from kiwifruit.
Authors: Hamiaux, C. / Maddumage, R. / Middleditch, M.J. / Prakash, R. / Brummell, D.A. / Baker, E.N. / Atkinson, R.G.
History
DepositionMay 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Nov 22, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_nat / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kiwellin
B: Kiwellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6134
Polymers39,5422
Non-polymers712
Water2,630146
1
A: Kiwellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8062
Polymers19,7711
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kiwellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8062
Polymers19,7711
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.420, 59.700, 54.550
Angle α, β, γ (deg.)90.000, 97.450, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A & B

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Components

#1: Protein Kiwellin


Mass: 19770.816 Da / Num. of mol.: 2 / Fragment: UNP residues 25-213 / Source method: isolated from a natural source / Details: fruit tissue / Source: (natural) Actinidia chinensis (golden kiwifruit) / Tissue: fruit tissue without skin / References: UniProt: L7TT83, UniProt: P85261*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.14 Å3/Da / Density % sol: 42.6 % / Description: thin plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 0.05 M KSCN, 27% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.05→40.08 Å / Num. all: 20381 / Num. obs: 20381 / % possible obs: 96.9 % / Redundancy: 7 % / Biso Wilson estimate: 23.7 Å2 / Rpim(I) all: 0.056 / Rrim(I) all: 0.151 / Rsym value: 0.14 / Net I/av σ(I): 4.423 / Net I/σ(I): 9.9 / Num. measured all: 141651
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
2.05-2.166.90.7090.65732022529340.2640.7090.6571396.3
2.16-2.297.10.520.4831.41995627990.1910.520.4834.196.4
2.29-2.457.10.4040.3751.81868726150.1490.4040.375596.8
2.45-2.657.10.2640.2452.81749024640.0970.2640.2456.997
2.65-2.97.10.1870.1743.91604922760.0690.1870.174997.2
2.9-3.2470.1390.1295.21430820530.0520.1390.12912.497.4
3.24-3.746.90.0860.087.81253918180.0320.0860.0818.197.4
3.74-4.586.70.0720.0679.21032515440.0280.0720.06721.297.6
4.58-6.486.10.0720.0668.7724311900.0290.0720.0662096.4
6.48-40.08470.070.0648.548296880.0260.070.06423.797.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
iMOSFLMdata reduction
SCALA3.3.16data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D30

3d30


Resolution: 2.05→40.08 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.2165 / WRfactor Rwork: 0.1872 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8217 / SU B: 10.072 / SU ML: 0.134 / SU R Cruickshank DPI: 0.197 / SU Rfree: 0.1642 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 1034 5.1 %RANDOM
Rwork0.1933 19316 --
obs0.195 20350 96.39 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 127.11 Å2 / Biso mean: 36.5693 Å2 / Biso min: 15.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20.84 Å2
2---3.48 Å20 Å2
3---4.81 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 2 146 2329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192231
X-RAY DIFFRACTIONr_bond_other_d0.0030.021986
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9363028
X-RAY DIFFRACTIONr_angle_other_deg0.84934615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6855294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01925.16193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02915349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4251511
X-RAY DIFFRACTIONr_chiral_restr0.080.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212596
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02481
X-RAY DIFFRACTIONr_mcbond_it2.5831.8561188
X-RAY DIFFRACTIONr_mcbond_other2.571.8541187
X-RAY DIFFRACTIONr_mcangle_it4.0722.7661478
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 83 -
Rwork0.291 1414 -
all-1497 -
obs--96.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.62391.2008-0.70753.3182-4.43610.34240.26350.18620.26370.30430.51780.68570.1249-0.4814-0.78130.54240.0081-0.07330.53310.09980.199529.1013.99629.788
23.34040.34861.03132.56190.09692.40560.0304-0.12860.16110.1545-0.05510.0209-0.1342-0.04630.02470.13220.0047-0.01860.07730.00010.013224.5136.3017.891
33.92980.5372-1.32761.96590.17242.31020.0766-0.1121-0.16810.153-0.05410.06370.13830.0218-0.02260.13190.0047-0.03230.0383-0.00160.02371.65925.8847.961
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 39
2X-RAY DIFFRACTION2A48 - 189
3X-RAY DIFFRACTION3B48 - 189

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