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- PDB-6th5: Crystal structure of mature wildtype primitive Phytochelatin synt... -

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Basic information

Entry
Database: PDB / ID: 6th5
TitleCrystal structure of mature wildtype primitive Phytochelatin synthase from Nostoc spec. - Alr0975
ComponentsAlr0975 protein
KeywordsTRANSFERASE / Phytochelatin / heavy-metal detoxification / glutathione / gamma-glutamyl cysteine
Function / homology
Function and homology information


glutathione gamma-glutamylcysteinyltransferase / glutathione gamma-glutamylcysteinyltransferase activity / phytochelatin biosynthetic process / response to metal ion / metal ion binding
Similarity search - Function
Phytochelatin synthase, N-terminal catalytic domain / Phytochelatin synthase, N-terminal domain superfamily / Phytochelatin synthase / Phytochelatin synthase / Phytochelatin synthase (PCS) domain profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
glutathione gamma-glutamylcysteinyltransferase
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsFeiler, C.G. / Blankenfeldt, W.
CitationJournal: To Be Published
Title: Crystal structure of mature wildtype primitive Phytochelatin synthase from Nostoc spec. - Alr0975
Authors: Feiler, C.G. / Blankenfeldt, W.
History
DepositionNov 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alr0975 protein
B: Alr0975 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4887
Polymers49,2882
Non-polymers2005
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-47 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.356, 46.670, 68.583
Angle α, β, γ (deg.)90.000, 92.258, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Alr0975 protein / Primitive phytochelatin synthase


Mass: 24643.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Gene: alr0975, alr0975 / Plasmid: p10$ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YY76
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 16% PEG 8000, 0.1 M MES pH 5.5, 0.2 M calcium acetate
PH range: 5-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 15, 2012
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.99→34.26 Å / Num. obs: 26211 / % possible obs: 97.38 % / Redundancy: 2.2 % / Biso Wilson estimate: 20.61 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.0975 / Rrim(I) all: 0.151 / Net I/σ(I): 6.59
Reflection shellResolution: 1.99→2.061 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 4465 / CC1/2: 0.845 / Rpim(I) all: 0.57 / Rrim(I) all: 0.879 / % possible all: 98.45

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BTW

2btw


Resolution: 1.99→34.26 Å / SU ML: 0.2406 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1224
RfactorNum. reflection% reflection
Rfree0.2383 1300 4.96 %
Rwork0.1993 --
obs0.2013 26210 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.53 Å2
Refinement stepCycle: LAST / Resolution: 1.99→34.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 0 5 317 3698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00553472
X-RAY DIFFRACTIONf_angle_d0.55434713
X-RAY DIFFRACTIONf_chiral_restr0.0445534
X-RAY DIFFRACTIONf_plane_restr0.0033612
X-RAY DIFFRACTIONf_dihedral_angle_d22.3563473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.070.31291370.28212787X-RAY DIFFRACTION98.38
2.07-2.160.32871470.26722736X-RAY DIFFRACTION98.3
2.16-2.280.31131570.24312788X-RAY DIFFRACTION98.17
2.28-2.420.26861460.23512752X-RAY DIFFRACTION98.04
2.42-2.610.26481210.22842784X-RAY DIFFRACTION97.98
2.61-2.870.28351550.22152760X-RAY DIFFRACTION97.59
2.87-3.280.22031500.18782778X-RAY DIFFRACTION97.83
3.28-4.140.18391440.15312755X-RAY DIFFRACTION96.15
4.14-34.260.18981430.16052771X-RAY DIFFRACTION94.55

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