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- PDB-8bv9: Acylphosphatase from E. coli -

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Basic information

Entry
Database: PDB / ID: 8bv9
TitleAcylphosphatase from E. coli
ComponentsAcylphosphatase
KeywordsHYDROLASE / ALPHA AND BETA PROTEINS / AMYLOID / PHOSPHATASE / Intertwined
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity
Similarity search - Function
Acylphosphatase, bacteria / Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.552 Å
AuthorsGavira, J.A. / Martinez-Rodriguez, S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-116261GB-I00 Spain
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: First 3-D structural evidence of a native-like intertwined dimer in the acylphosphatase family.
Authors: Martinez-Rodriguez, S. / Camara-Artigas, A. / Gavira, J.A.
History
DepositionJan 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Nov 5, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_modification_feature.label_seq_id / _pdbx_modification_feature.modified_residue_label_seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _reflns.d_resolution_low / _software.version / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Chirality error
Details: The most important reason for the correction is the Cis/Trans isomer of Pro79.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9007
Polymers10,4261
Non-polymers4746
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-34 kcal/mol
Surface area6480 Å2
Unit cell
Length a, b, c (Å)40.415, 81.944, 63.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Acylphosphatase / Acylphosphate phosphohydrolase


Mass: 10425.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yccX, Z1320, ECs1052 / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AB66, acylphosphatase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.34 Å3/Da / Density % sol: 47.4 % / Description: Neddle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M AS 30% w/v PEG4K / PH range: 4.0-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 18, 2021
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.55→41.97 Å / Num. obs: 3631 / % possible obs: 99 % / Redundancy: 6.5 % / Biso Wilson estimate: 68.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.053 / Rrim(I) all: 0.109 / Net I/σ(I): 10.2
Reflection shellResolution: 2.55→2.67 Å / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 431 / CC1/2: 0.44

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.552→41.006 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.89 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.953 / ESU R Free: 0.349
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2782 162 4.463 %RANDOM
Rwork0.2049 3468 --
all0.208 ---
obs-3630 98.534 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 67.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.259 Å20 Å20 Å2
2--2.055 Å20 Å2
3----0.796 Å2
Refinement stepCycle: LAST / Resolution: 2.552→41.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms732 0 27 10 769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.012807
X-RAY DIFFRACTIONr_bond_other_d0.0010.016773
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.8621085
X-RAY DIFFRACTIONr_angle_other_deg0.5481.7831773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3165100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.118511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79510143
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.5751038
X-RAY DIFFRACTIONr_chiral_restr0.0680.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02202
X-RAY DIFFRACTIONr_nbd_refined0.1930.2117
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.2599
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2347
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2421
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.234
X-RAY DIFFRACTIONr_nbd_other0.1610.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3660.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0230.23
X-RAY DIFFRACTIONr_mcbond_it6.0336.167385
X-RAY DIFFRACTIONr_mcbond_other5.9886.168385
X-RAY DIFFRACTIONr_mcangle_it8.53811.12484
X-RAY DIFFRACTIONr_mcangle_other8.54411.123485
X-RAY DIFFRACTIONr_scbond_it7.787.38422
X-RAY DIFFRACTIONr_scbond_other7.5937.283411
X-RAY DIFFRACTIONr_scangle_it11.98813.15599
X-RAY DIFFRACTIONr_scangle_other11.7112.975582
X-RAY DIFFRACTIONr_lrange_it15.20566.988815
X-RAY DIFFRACTIONr_lrange_other15.19666.981816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.552-2.6180.365170.3362380.3382570.9170.93399.22180.306
2.618-2.6890.652110.3112580.3222690.7880.9361000.271
2.689-2.7670.452130.2982180.3062320.840.94399.5690.26
2.767-2.8510.278110.2972440.2962560.9460.93799.60940.241
2.851-2.9440.33150.3022310.3032370.9380.93799.57810.241
2.944-3.0470.497100.2422200.2522320.9210.95999.13790.203
3.047-3.1620.37990.2392060.2452170.9190.95899.07830.204
3.162-3.290.319120.1982050.2042180.9450.97499.54130.171
3.29-3.4350.11270.21970.1972060.9950.97299.02910.193
3.435-3.6020.33980.2091830.2141990.8980.97195.97990.191
3.602-3.7950.22290.1851610.1871870.9740.98490.90910.188
3.795-4.0230.34670.2131710.2181800.9430.97298.88890.201
4.023-4.2980.192110.1711570.1731680.9870.9861000.169
4.298-4.6380.1760.1381580.141650.9950.98999.39390.137
4.638-5.0740.34750.1591470.1621530.9190.98699.34640.166
5.074-5.6620.33970.1441260.1521340.960.98799.25370.144
5.662-6.5170.30330.231150.2311210.9770.97497.52070.239
6.517-7.9320.07630.2051000.2011040.9860.97399.03850.202
7.932-11.0130.29250.165790.171870.9710.98396.55170.182
11.013-41.0060.6730.364540.369610.7730.92693.44260.386

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