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- PDB-8f9x: Cyclase-Phosphotriesterase from Ruegeria pomeroyi DSS-3 -

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Basic information

Entry
Database: PDB / ID: 8f9x
TitleCyclase-Phosphotriesterase from Ruegeria pomeroyi DSS-3
ComponentsCyclase family protein
KeywordsHYDROLASE / cyclase / phosphotriesterase / organophosphates / OP-hydrolase / Zn-dependent enzyme
Function / homologyKynurenine formamidase/cyclase-like / Kynurenine formamidase superfamily / Putative cyclase / arylformamidase activity / L-tryptophan catabolic process to kynurenine / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / metal ion binding / Cyclase family protein
Function and homology information
Biological speciesRuegeria pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsFrkic, R.L. / Ji, D. / Jackson, C.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: Chembiochem / Year: 2025
Title: A Thermostable Bacterial Metallohydrolase that Degrades Organophosphate Plasticizers.
Authors: Ji, D. / Frkic, R.L. / Delyami, J. / Larsen, J.S. / Spence, M.A. / Jackson, C.J.
History
DepositionNov 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 2.0Jan 29, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / entity / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct / struct_asym / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _audit_author.identifier_ORCID / _audit_author.name ..._audit_author.identifier_ORCID / _audit_author.name / _entity.pdbx_number_of_molecules / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _struct.title / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet.number_strands
Description: Atomic clashes / Provider: author / Type: Coordinate replacement
Revision 2.1Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclase family protein
B: Cyclase family protein
C: Cyclase family protein
D: Cyclase family protein
E: Cyclase family protein
F: Cyclase family protein
G: Cyclase family protein
H: Cyclase family protein
I: Cyclase family protein
J: Cyclase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,33275
Polymers242,66110
Non-polymers6,67165
Water2,612145
1
A: Cyclase family protein
B: Cyclase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,73313
Polymers48,5322
Non-polymers1,20111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-181 kcal/mol
Surface area17620 Å2
MethodPISA
2
C: Cyclase family protein
D: Cyclase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,77714
Polymers48,5322
Non-polymers1,24512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-135 kcal/mol
Surface area18440 Å2
MethodPISA
3
E: Cyclase family protein
F: Cyclase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,70715
Polymers48,5322
Non-polymers1,17513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-145 kcal/mol
Surface area19280 Å2
MethodPISA
4
G: Cyclase family protein
H: Cyclase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,92316
Polymers48,5322
Non-polymers1,39114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-221 kcal/mol
Surface area17950 Å2
MethodPISA
5
I: Cyclase family protein
J: Cyclase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,19217
Polymers48,5322
Non-polymers1,66015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-215 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.080, 68.080, 446.501
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Cyclase family protein


Mass: 24266.059 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi DSS-3 (bacteria) / Gene: SPO0761 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5LVE1

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Non-polymers , 6 types, 210 molecules

#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 26% PEG MME 550, 0.05 M CaCl2, 0.1M Bis-Tris 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.499
11K, H, -L20.501
ReflectionResolution: 2.32→34.35 Å / Num. obs: 100307 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.172 / Net I/σ(I): 8.4 / Num. measured all: 815856 / Scaling rejects: 188
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.32-2.3671.9843548750650.351.199.9
12.71-34.357.50.05345786080.99826.296.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALA0.7.9data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 2.32→34.04 Å / Cross valid method: THROUGHOUT / σ(F): 181.9 / Phase error: 30.17 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 5012 5 %RANDOM
Rwork0.2192 ---
obs0.2351 100145 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16924 0 358 145 17427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.615
X-RAY DIFFRACTIONf_dihedral_angle_d14.3086106
X-RAY DIFFRACTIONf_chiral_restr0.0472558
X-RAY DIFFRACTIONf_plane_restr0.0043204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.360.35552640.33084837X-RAY DIFFRACTION94
2.36-2.40.32691840.33644727X-RAY DIFFRACTION96
2.4-2.450.31772720.33854743X-RAY DIFFRACTION94
2.45-2.50.33062680.33634713X-RAY DIFFRACTION95
2.5-2.550.36622300.33084735X-RAY DIFFRACTION95
2.55-2.610.34582020.33584927X-RAY DIFFRACTION96
2.61-2.680.30442500.33794647X-RAY DIFFRACTION95
2.68-2.750.34532900.31974780X-RAY DIFFRACTION94
2.75-2.830.34932040.31594837X-RAY DIFFRACTION96
2.83-2.920.30242100.29784725X-RAY DIFFRACTION96
2.92-3.030.332440.3094751X-RAY DIFFRACTION95
3.03-3.150.32192540.28494746X-RAY DIFFRACTION95
3.15-3.290.30032210.25434806X-RAY DIFFRACTION96
3.29-3.460.25992660.23454772X-RAY DIFFRACTION95
3.47-3.680.29062200.22264755X-RAY DIFFRACTION96
3.68-3.970.26692660.21414752X-RAY DIFFRACTION95
3.97-4.360.23192680.18414735X-RAY DIFFRACTION95
4.36-4.990.23352940.16624710X-RAY DIFFRACTION94
4.99-6.280.22162730.18454749X-RAY DIFFRACTION95
6.29-34.040.2323320.20274686X-RAY DIFFRACTION93

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