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- PDB-8fzw: Thaumatin crystallized in cyclic olefin copolymer-based microflui... -

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Basic information

Entry
Database: PDB / ID: 8fzw
TitleThaumatin crystallized in cyclic olefin copolymer-based microfluidic chips
ComponentsThaumatin I
KeywordsPLANT PROTEIN / wild type
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLiu, Z. / Gu, K. / Shelby, M.L. / Gilbile, D. / Lyubimov, A.Y. / Russi, S. / Cohen, A.E. / Coleman, M.A. / Frank, M. / Kuhl, T.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Department of Energy (DOE, United States) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: A user-friendly plug-and-play cyclic olefin copolymer-based microfluidic chip for room-temperature, fixed-target serial crystallography.
Authors: Liu, Z. / Gu, K.K. / Shelby, M.L. / Gilbile, D. / Lyubimov, A.Y. / Russi, S. / Cohen, A.E. / Narayanasamy, S.R. / Botha, S. / Kupitz, C. / Sierra, R.G. / Poitevin, F. / Gilardi, A. / Lisova, ...Authors: Liu, Z. / Gu, K.K. / Shelby, M.L. / Gilbile, D. / Lyubimov, A.Y. / Russi, S. / Cohen, A.E. / Narayanasamy, S.R. / Botha, S. / Kupitz, C. / Sierra, R.G. / Poitevin, F. / Gilardi, A. / Lisova, S. / Coleman, M.A. / Frank, M. / Kuhl, T.L.
History
DepositionJan 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thaumatin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3932
Polymers22,2431
Non-polymers1501
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.666, 58.666, 151.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

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Components

#1: Protein Thaumatin I / Thaumatin-1


Mass: 22243.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 1 M L-sodium potassium tartrate with 0.1 M ADA buffer (pH 6-6.5)
PH range: 6-6.5

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.48→36.39 Å / Num. obs: 45060 / % possible obs: 99.87 % / Redundancy: 10.3 % / Biso Wilson estimate: 19.67 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1195 / Rpim(I) all: 0.03894 / Rrim(I) all: 0.1259 / Net I/σ(I): 10.89
Reflection shellResolution: 1.48→1.533 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.937 / Mean I/σ(I) obs: 0.89 / Num. unique obs: 4434 / CC1/2: 0.572 / CC star: 0.853 / Rpim(I) all: 0.6175 / Rrim(I) all: 2.035 / % possible all: 99.95
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→36.39 Å / SU ML: 0.1482 / Cross valid method: FREE R-VALUE / Phase error: 15.0133
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1574 2000 4.44 %
Rwork0.1426 43056 -
obs0.1433 45060 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.24 Å2
Refinement stepCycle: LAST / Resolution: 1.48→36.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 10 147 1709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631642
X-RAY DIFFRACTIONf_angle_d0.93252230
X-RAY DIFFRACTIONf_chiral_restr0.0778242
X-RAY DIFFRACTIONf_plane_restr0.0127294
X-RAY DIFFRACTIONf_dihedral_angle_d12.412597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.3181390.30283005X-RAY DIFFRACTION99.94
1.52-1.560.27711410.25973035X-RAY DIFFRACTION100
1.56-1.60.23811390.2283011X-RAY DIFFRACTION100
1.6-1.660.23751410.20523023X-RAY DIFFRACTION100
1.66-1.710.21281400.19073025X-RAY DIFFRACTION99.97
1.71-1.780.19551420.1823052X-RAY DIFFRACTION99.97
1.78-1.860.16851410.1623022X-RAY DIFFRACTION100
1.86-1.960.15731420.13633082X-RAY DIFFRACTION100
1.96-2.090.14321430.12533056X-RAY DIFFRACTION100
2.09-2.250.13871420.13233075X-RAY DIFFRACTION100
2.25-2.470.17071430.12973083X-RAY DIFFRACTION100
2.47-2.830.16121450.14083105X-RAY DIFFRACTION99.75
2.83-3.560.15321460.13893162X-RAY DIFFRACTION99.97
3.57-36.390.11951560.11483320X-RAY DIFFRACTION98.86
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)
10.439908960651-0.3427671771470.201430346080.3309600871590.0009720131564140.4549328127190.07460085863840.0694134754121-0.0627557349808-0.0716973235873-0.02727273793090.04276135727610.10761199183-0.08798333082715.19558703024E-60.169539294103-0.0287063744088-0.01948907642860.184606258940.01029950270370.174737835171-7.2501064941413.6564688146-15.213246077
20.350127700534-0.140158244244-0.1931802132570.9236140599750.1066591748770.106770477553-0.0476830163231-0.123855083902-0.147619536255-0.0989608462165-0.05650874627550.003965044245750.102595366757-0.142704275864-0.01881654177170.160902032648-0.0761253865117-0.007850383529590.2489595226930.03834782338390.196480265752-16.4839062269.83324503477-10.2656120476
30.620223996253-0.2774824599610.4248663451330.320191043994-0.3772706898270.4726224957410.1020948270290.000579981567702-0.153661925138-0.0554737169629-0.04383469347270.004793378409260.1472817337630.002283515772154.56512097345E-50.176666783912-0.00981600162992-0.01920380333410.156678238465-0.003126021090130.202606601109-0.0366271918458.79330205618-10.1129531611
40.3403002118040.3363252758860.1232428404440.350144438385-0.0284963491230.887297005104-0.0144142913559-0.09340555629970.09977134279930.0656062255259-0.008656291076130.0511485101635-0.119705125881-0.1390377230351.65787980094E-50.1309206623210.00310716961882-0.00945511863470.1994511399330.006086979388410.169669319151-8.2388851587722.0563957431-3.3101775324
50.473749579258-0.1503861571840.4730530332770.406818908807-0.05369382435960.487674180095-0.05005235339340.01567494354030.001437833217620.01628439718810.0620373796995-0.01219470101340.01137473650230.0621933746365-1.24619270201E-50.183410200729-0.00216972167921-0.009800934749850.166442044593-0.009024707665020.1633211112355.0426820080920.61621285067.01959597448
60.48153445040.1183479178290.2089590244840.317788778624-0.2130263713990.335065150091-0.0418002734302-0.07738768522390.06773225189080.02196472198010.03372752805530.0310341106012-0.114088915393-0.229477812831-4.57707611648E-50.1570857351070.00180222510022-0.01184767435760.2546834163650.001375699968850.184348366152-10.848397168322.8596489817-2.07320307885
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 35 )1 - 351 - 35
22chain 'A' and (resid 36 through 47 )36 - 4736 - 47
33chain 'A' and (resid 48 through 91 )48 - 9148 - 91
44chain 'A' and (resid 92 through 138 )92 - 13892 - 138
55chain 'A' and (resid 139 through 176 )139 - 176139 - 176
66chain 'A' and (resid 177 through 207 )177 - 207177 - 207

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