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- PDB-3o0f: Crystal structure of a putative metal-dependent phosphoesterase (... -

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Basic information

Entry
Database: PDB / ID: 3o0f
TitleCrystal structure of a putative metal-dependent phosphoesterase (BAD_1165) from bifidobacterium adolescentis atcc 15703 at 1.94 A resolution
Componentsputative metal-dependent phosphoesterase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
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
ADENOSINE MONOPHOSPHATE / : / PHOSPHATE ION / Polymerase/histidinol phosphatase N-terminal domain-containing protein
Similarity search - Component
Biological speciesBifidobacterium adolescentis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 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 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references / Structure summary
Revision 1.3Nov 16, 2011Group: Structure summary
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _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: putative metal-dependent phosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6088
Polymers32,8651
Non-polymers7437
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.341, 103.341, 54.744
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 (bacteria)
Strain: ATCC 15703 / DSM 20083 / Gene: BAD_1165 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1A2L3

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Non-polymers , 6 types, 190 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.71
Details: 24.0000% 2-methyl-2,4-pentanediol, 0.0200M calcium acetate, 0.1M sodium acetate pH 4.71, 0.005 M adenosine 5'-monophosphate, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2010
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.94→44.748 Å / Num. obs: 24784 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.988 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 12.54
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.94-2.010.7992.6178272431197.7
2.01-2.090.6944.12334024591100
2.09-2.180.5745.42740923531100
2.18-2.30.5156.8285012548198.7
2.3-2.440.3488.12838824071100
2.44-2.630.3019.62933525111100
2.63-2.90.213.22947825251100
2.9-3.310.12818.42839824431100
3.31-4.170.09325.1277322527199.9
4.17-44.7480.06430.6284182580199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→44.748 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.697 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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 RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. (4). WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. (5) ADENOSINE MONOPHOSPHATE (AMP) IS MODELED BASED ON CO-CRYSTALLIZATION CONDTION. (6). 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. (7). AN 1,2-ETHANEDIOL (EDO) MOLECULE WAS MODELED BASED ON CRYO CONDITION. (8). PO4 ION WERE MODELED BASED ON THE ELECTRON DENSITY, COORDINATION GEOMETRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 1241 5 %RANDOM
Rwork0.1597 ---
obs0.1613 24761 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.62 Å2 / Biso mean: 23.7813 Å2 / Biso min: 5.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.2 Å20 Å2
2--0.41 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.94→44.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 39 183 2373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212301
X-RAY DIFFRACTIONr_bond_other_d0.0010.021496
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9613148
X-RAY DIFFRACTIONr_angle_other_deg1.17633650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.823.824102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01815349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7171518
X-RAY DIFFRACTIONr_chiral_restr0.1320.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
X-RAY DIFFRACTIONr_mcbond_it1.97331465
X-RAY DIFFRACTIONr_mcbond_other0.5933598
X-RAY DIFFRACTIONr_mcangle_it3.24552357
X-RAY DIFFRACTIONr_scbond_it5.7268836
X-RAY DIFFRACTIONr_scangle_it7.98911791
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 83 -
Rwork0.231 1694 -
all-1777 -
obs--96.79 %
Refinement TLS params.Method: refined / Origin x: 29.3273 Å / Origin y: 28.9665 Å / Origin z: 7.3925 Å
111213212223313233
T0.0216 Å20.0212 Å2-0.011 Å2-0.0365 Å2-0.0199 Å2--0.0213 Å2
L0.7281 °2-0.3443 °20.0941 °2-0.9512 °2-0.0097 °2--0.6733 °2
S0.0149 Å °0.0394 Å °-0.1051 Å °-0.0182 Å °-0.034 Å °0.0585 Å °0.0044 Å °-0.0525 Å °0.0191 Å °

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