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- PDB-2btw: Crystal structure of Alr0975 -

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Basic information

Entry
Database: PDB / ID: 2btw
TitleCrystal structure of Alr0975
Components(ALR0975 PROTEIN) x 2
KeywordsTRANSFERASE / PHYTOCHELATIN SYNTHASE / PCS / ALR0975 / 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
glutathione gamma-glutamylcysteinyltransferase
Similarity search - Component
Biological speciesANABAENA SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 7, 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 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
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_entry_details.has_protein_modification / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)58,9274
Polymers58,8462
Non-polymers802
Water4,648258
1
A: ALR0975 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4772
Polymers29,4371
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ALR0975 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4492
Polymers29,4091
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.860, 62.467, 76.552
Angle α, β, γ (deg.)90.00, 101.38, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.00015, 0.00054), (0.00014, -0.99998, -0.00683), (0.00054, -0.00683, 0.99998)
Vector: 56.65526, 52.43811, 0.17243)

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Components

#1: Protein ALR0975 PROTEIN / PRIMITIVE PHYTOCHELATIN SYNTHASE


Mass: 29437.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7120 / Plasmid: PJC40 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8YY76, glutathione gamma-glutamylcysteinyltransferase
#2: Protein ALR0975 PROTEIN / PRIMITIVE PHYTOCHELATIN SYNTHASE


Mass: 29409.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7120 / Plasmid: PJC40 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8YY76, glutathione gamma-glutamylcysteinyltransferase
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PUTATIVE N-TERMINAL SECRETION SIGNAL WAS NOT INCLUDED IN THE 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: 2.23 Å3/Da / Density % sol: 44.32 %
Crystal growpH: 5 / Details: pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97935,0.974
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 16, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.9741
ReflectionResolution: 2.05→18 Å / Num. obs: 27903 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→19.1 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.891 / SU B: 8.084 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ELECTRON DENSITY IS MISSING FOR THE TAG AND THE FOUR N-TERMINAL RESIDUES AS WELL AS THE THREE C-TERMINAL RESIDUES
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1503 5.1 %RANDOM
Rwork0.2 ---
obs0.203 28173 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.02 Å2
2--0.06 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 2 258 3598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223404
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.9474609
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2071.52173
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68523392
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.13131428
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4214.51217
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.333 98
Rwork0.224 1975
Refinement TLS params.Method: refined / Origin x: 28.3166 Å / Origin y: 26.1328 Å / Origin z: 21.015 Å
111213212223313233
T0.0044 Å20.0116 Å20.0037 Å2-0.0246 Å2-0.0003 Å2--0.0358 Å2
L0.0028 °20.0055 °20.0266 °2-0.0109 °20.0517 °2--0.2489 °2
S0.0112 Å °0.0154 Å °-0.0104 Å °-0.0548 Å °-0.0105 Å °-0.0118 Å °-0.0041 Å °0.0122 Å °-0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 238
2X-RAY DIFFRACTION1B29 - 238

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