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- PDB-2bu3: Acyl-enzyme intermediate between Alr0975 and glutathione at pH 3.4 -

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Basic information

Entry
Database: PDB / ID: 2bu3
TitleAcyl-enzyme intermediate between Alr0975 and glutathione at pH 3.4
ComponentsALR0975 PROTEIN
KeywordsTRANSFERASE / PHYTOCHELATIN SYNTHASE / PCS / ALR0975 / ACYL-ENZYME INTERMEDIATE / NOSTOC / GLUTATHIONE METABOLISM / CYSTEINE PROTEASE
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 domain / Phytochelatin synthase, N-terminal catalytic domain / Phytochelatin synthase, N-terminal domain superfamily / Phytochelatin synthase / Phytochelatin synthase / Phytochelatin synthase (PCS) domain profile. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
GAMMA-GLUTAMYLCYSTEINE / glutathione gamma-glutamylcysteinyltransferase
Similarity search - Component
Biological speciesANABAENA SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVivares, D. / Arnoux, P. / Pignol, D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: A Papain-Like Enzyme at Work: Native and Acyl- Enzyme Intermediate Structures in Phytochelatin Synthesis.
Authors: Vivares, D. / Arnoux, P. / Pignol, D.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Characterization of Phytochelatin Synthase-Like Protein Encoded by Alr0975 from a Prokaryote, Nostoc Sp. Pcc 7120
Authors: Tsuji, N. / Nishikori, S. / Iwabe, O. / Shiraki, K. / Miyasaka, H. / Takagi, M. / Hirata, K. / Miyamoto, K.
#2: Journal: Phytochemistry / Year: 2004
Title: A Cyanobacterial Protein with Similarity to Phytochelatin Synthases Catalyzes the Conversion of Glutathione to Gamma-Glutamylcysteine and Lacks Phytochelatin Synthase Activity
Authors: Harada, E. / Von Roepenack-Lahaye, E. / Clemens, S.
History
DepositionJun 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Nov 6, 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: ALR0975 PROTEIN
B: ALR0975 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5268
Polymers58,8742
Non-polymers6526
Water6,990388
1
A: ALR0975 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7634
Polymers29,4371
Non-polymers3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ALR0975 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7634
Polymers29,4371
Non-polymers3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.253, 58.259, 72.561
Angle α, β, γ (deg.)90.00, 108.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.51157, 0.53057, 0.67586), (0.49733, -0.82427, 0.27064), (0.70068, 0.19767, -0.68554)
Vector: -18.83119, 8.77481, 33.24425)

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Components

#1: Protein ALR0975 PROTEIN / PRIMITIVE PHYTOCHELATIN SYNTHASE


Mass: 29437.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA SP. (bacteria) / Plasmid: PJC40 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8YY76, glutathione gamma-glutamylcysteinyltransferase
#2: Chemical ChemComp-3GC / GAMMA-GLUTAMYLCYSTEINE


Mass: 250.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14N2O5S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PUTATIVE N-TERMINAL SECRETION SIGNAL WAS NOT INCLUDED IN THE PLASMID CONSTRUCTION

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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: 2.21 Å3/Da / Density % sol: 43.94 %
Crystal growpH: 3.2 / Details: pH 3.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.4→29 Å / Num. obs: 87418 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BTW

2btw


Resolution: 1.4→29.59 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.477 / SU ML: 0.031 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ARGININE 180 IS DISORDERED AND WAS MODELED AS A GLYCINE
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1744 2 %RANDOM
Rwork0.174 ---
obs0.174 85298 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.02 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 34 388 3627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223299
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9544453
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6945399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41624.367158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00515573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1151521
X-RAY DIFFRACTIONr_chiral_restr0.0810.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022483
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.21613
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22330
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.711.52061
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08723243
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.77431393
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7284.51210
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.232 109
Rwork0.216 6128
Refinement TLS params.Method: refined / Origin x: 1.961 Å / Origin y: 8.637 Å / Origin z: 21.588 Å
111213212223313233
T0.0084 Å20.0033 Å20.0023 Å2--0.0075 Å20.0003 Å2--0.0126 Å2
L0.0746 °20.1083 °2-0.095 °2-0.3077 °2-0.3186 °2--0.5338 °2
S-0.0118 Å °-0.0085 Å °-0.0197 Å °-0.0135 Å °-0.0124 Å °-0.0389 Å °-0.0063 Å °0.0258 Å °0.0242 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 239
2X-RAY DIFFRACTION1B32 - 239

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