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- PDB-2pau: Crystal structure of the 5'-deoxynucleotidase YfbR mutant E72A co... -

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Basic information

Entry
Database: PDB / ID: 2pau
TitleCrystal structure of the 5'-deoxynucleotidase YfbR mutant E72A complexed with Co(2+) and dAMP
Components5'-deoxynucleotidase YfbR
KeywordsHYDROLASE / Nucleotidase / 5'-deoxynucleotidase / YfbR / HD domain phosphohydrolase
Function / homology
Function and homology information


pyrimidine deoxyribonucleotide salvage / thymidylate 5'-phosphatase activity / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / dUMP biosynthetic process / cobalt ion binding / nucleotide binding / identical protein binding / cytoplasm
Similarity search - Function
5'-deoxynucleotidase YfbR / 5'-deoxynucleotidase YfbR-like / 5'-deoxynucleotidase YfbR/HDDC2 / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain ...5'-deoxynucleotidase YfbR / 5'-deoxynucleotidase YfbR-like / 5'-deoxynucleotidase YfbR/HDDC2 / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / 5'-deoxynucleotidase YfbR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZimmerman, M.D. / Proudfoot, M. / Yakunin, A. / Minor, W.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli.
Authors: Zimmerman, M.D. / Proudfoot, M. / Yakunin, A. / Minor, W.
History
DepositionMar 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-deoxynucleotidase YfbR
B: 5'-deoxynucleotidase YfbR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6357
Polymers45,7482
Non-polymers8865
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-52 kcal/mol
Surface area15010 Å2
MethodPISA
2
A: 5'-deoxynucleotidase YfbR
B: 5'-deoxynucleotidase YfbR
hetero molecules

A: 5'-deoxynucleotidase YfbR
B: 5'-deoxynucleotidase YfbR
hetero molecules

A: 5'-deoxynucleotidase YfbR
B: 5'-deoxynucleotidase YfbR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,90521
Polymers137,2456
Non-polymers2,65915
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)135.595, 135.595, 54.936
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: D5M / End label comp-ID: D5M / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
14SERSERAA - D4 - 3016
22LYSLYSBB - G2 - 3014

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Components

#1: Protein 5'-deoxynucleotidase YfbR / Nucleoside 5'-monophosphate phosphohydrolase / 5'-deoxyribonucleotidase


Mass: 22874.219 Da / Num. of mol.: 2 / Mutation: E72A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yfbR, b2291, JW2288 / Plasmid: Modified pET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: P76491, 5'-nucleotidase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O6P
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M NH4 Citrate, 0.1 % w/v NDSB 256, 5 % w/v PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2006
Details: LN2 cooled first crystal, sagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits
RadiationMonochromator: Rosenbaum-Rock high-resolution Si(111) double-crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 25437 / Num. obs: 25437 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 9.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2 / Rsym value: 0.563 / % possible all: 82.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
REFMAC5.2.0005refinement
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WPH

1wph
PDB Unreleased entry


Resolution: 2.1→40.13 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.201 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.259 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COOT program has also been used in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1028 5.1 %RANDOM
Rwork0.193 ---
all0.196 19971 --
obs0.196 19971 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 53 53 2830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212825
X-RAY DIFFRACTIONr_bond_other_d0.0020.022577
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.983830
X-RAY DIFFRACTIONr_angle_other_deg0.90235943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10824.231130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35115464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8211519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02560
X-RAY DIFFRACTIONr_nbd_refined0.2380.2690
X-RAY DIFFRACTIONr_nbd_other0.1830.22573
X-RAY DIFFRACTIONr_nbtor_refined0.190.21373
X-RAY DIFFRACTIONr_nbtor_other0.0930.21686
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3370.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.330.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9831.51819
X-RAY DIFFRACTIONr_mcbond_other0.2761.5706
X-RAY DIFFRACTIONr_mcangle_it1.4522805
X-RAY DIFFRACTIONr_scbond_it2.41131147
X-RAY DIFFRACTIONr_scangle_it3.6154.51025
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2618 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.510.5
medium thermal0.792
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 72 -
Rwork0.25 1270 -
obs--82.74 %

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