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- PDB-3e0f: Crystal structure of a putative metal-dependent phosphoesterase (... -

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Basic information

Entry
Database: PDB / ID: 3e0f
TitleCrystal structure of a putative metal-dependent phosphoesterase (bad_1165) from bifidobacterium adolescentis atcc 15703 at 2.40 A resolution
ComponentsPutative Metal-dependent Phosphoesterase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / 5'-3' DNA exonuclease activity / nucleotide binding / metal ion binding
Similarity search - Function
DNA polymerase; domain 1 - #650 / : / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / DNA polymerase; domain 1 / TIM Barrel ...DNA polymerase; domain 1 - #650 / : / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / DNA polymerase; domain 1 / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / PHOSPHATE ION / Polymerase/histidinol phosphatase N-terminal domain-containing protein
Similarity search - Component
Biological speciesBifidobacterium adolescentis ATCC 15703 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity.
Authors: Han, G.W. / Ko, J. / Farr, C.L. / Deller, M.C. / Xu, Q. / Chiu, H.J. / Miller, M.D. / Sefcikova, J. / Somarowthu, S. / Beuning, P.J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S. ...Authors: Han, G.W. / Ko, J. / Farr, C.L. / Deller, M.C. / Xu, Q. / Chiu, H.J. / Miller, M.D. / Sefcikova, J. / Somarowthu, S. / Beuning, P.J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A. / Ondrechen, M.J.
History
DepositionJul 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 20, 2011Group: Database references / Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Putative Metal-dependent Phosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2917
Polymers32,8651
Non-polymers4266
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.460, 102.460, 54.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative Metal-dependent Phosphoesterase


Mass: 32864.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium adolescentis ATCC 15703 (bacteria)
Gene: YP_910028.1, BAD_1165 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1A2L3

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Non-polymers , 5 types, 109 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.0200M CaCl2, 30.0000% MPD, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 26, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→29.579 Å / Num. obs: 12857 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.482 Å2 / Rmerge(I) obs: 0.119
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.4-2.490.5252.796952601199.3
2.49-2.580.4823.8114072262199.4
2.58-2.70.3885145512539199.8
2.7-2.840.36.1139442425199.8
2.84-3.020.2197.8145262517199.6
3.02-3.250.16310143152482199.9
3.25-3.580.11813.1144972518199.8
3.58-4.090.08117141872464199.9
4.09-5.140.06719.7143672494199.8
5.14-29.5790.05621.9146302541199.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→29.579 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.928 / SU B: 12.405 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.221
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (4). THE PRESENCE OF ZINC AND IRON WERE CONFIRMED BY X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS. THE METAL IDENTITY AT THE INDIVIDUAL ZN AND FE SITES WAS BASED ON ANOMALOUS DIFFERENCE FOURIER MAP COMPARISONS WITH DATA COLLECTED ABOVE AND BELOW THE FOLLOWING K ABSORPTION EDGES: FE AND ZN. (5). AN ACETATE (ACT) ION WAS MODELED BASED ON CRYSTALLIZATION CONDITION. (6). PO4 IONS WERE MODELED BASED ON THE ELECTRON DENSITY, COORDINATION GEOMETRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 626 4.9 %RANDOM
Rwork0.149 ---
obs0.152 12839 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.211 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.48 Å20 Å2
2--0.95 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 17 103 2274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212269
X-RAY DIFFRACTIONr_bond_other_d0.0010.021485
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9513101
X-RAY DIFFRACTIONr_angle_other_deg0.94333618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9065297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64123.529102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43515352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6461520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
X-RAY DIFFRACTIONr_nbd_refined0.20.2489
X-RAY DIFFRACTIONr_nbd_other0.1990.21593
X-RAY DIFFRACTIONr_nbtor_refined0.170.21135
X-RAY DIFFRACTIONr_nbtor_other0.0880.21217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.214
X-RAY DIFFRACTIONr_mcbond_it2.12231572
X-RAY DIFFRACTIONr_mcbond_other0.4363594
X-RAY DIFFRACTIONr_mcangle_it3.08752344
X-RAY DIFFRACTIONr_scbond_it5.5578871
X-RAY DIFFRACTIONr_scangle_it7.6311757
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 44 -
Rwork0.187 906 -
all-950 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 28.9331 Å / Origin y: 28.6887 Å / Origin z: 7.3071 Å
111213212223313233
T-0.0501 Å20.0289 Å2-0.017 Å2--0.0405 Å2-0.0057 Å2---0.0636 Å2
L0.7815 °2-0.3269 °2-0.0096 °2-1.0759 °20.3056 °2--0.7446 °2
S0.0423 Å °0.0296 Å °-0.0728 Å °-0.0341 Å °-0.052 Å °0.0978 Å °0.0504 Å °-0.0102 Å °0.0097 Å °

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