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

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Basic information

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


pyrimidine deoxyribonucleotide salvage / : / 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
: / DI(HYDROXYETHYL)ETHER / THYMIDINE-5'-PHOSPHATE / 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: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: 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.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.value / _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)46,6177
Polymers45,7482
Non-polymers8685
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-58 kcal/mol
Surface area14770 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)139,85121
Polymers137,2456
Non-polymers2,60515
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)136.136, 136.136, 55.418
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:

Component-ID: 2 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: TMP / End label comp-ID: TMP / Refine code: 4 / Auth seq-ID: 2 - 301 / Label seq-ID: 4

Dom-IDAuth asym-IDLabel asym-ID
1AA - D
2BB - G

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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-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P
#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.: 42 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M NH4 Citrate, 0.8 % w/v NDSB 256, 5 % w/v PEG 3350, 1 % v/v Glycerol, 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: 2.1→50 Å / Num. all: 22238 / Num. obs: 22238 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.8 / % possible all: 84

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
REFMAC5.2.0005refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WPH

1wph
PDB Unreleased entry


Resolution: 2.1→40.39 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 10.277 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.233 / ESU R Free: 0.198 / 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
Rfree0.247 1102 5.1 %RANDOM
Rwork0.194 ---
all0.196 21608 --
obs0.196 21608 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2741 0 51 42 2834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222840
X-RAY DIFFRACTIONr_bond_other_d0.0090.022605
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9753847
X-RAY DIFFRACTIONr_angle_other_deg0.93236013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21224.308130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28615474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1531517
X-RAY DIFFRACTIONr_chiral_restr0.1020.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
X-RAY DIFFRACTIONr_nbd_refined0.2320.2677
X-RAY DIFFRACTIONr_nbd_other0.1810.22590
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21368
X-RAY DIFFRACTIONr_nbtor_other0.0920.21662
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.320.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9261.51805
X-RAY DIFFRACTIONr_mcbond_other0.2761.5707
X-RAY DIFFRACTIONr_mcangle_it1.3622808
X-RAY DIFFRACTIONr_scbond_it2.40631160
X-RAY DIFFRACTIONr_scangle_it3.5184.51039
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: 2645 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.490.5
medium thermal0.742
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 72 -
Rwork0.201 1323 -
obs--83.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.36323.0676-2.58863.3582-1.60728.3110.19650.59020.2495-0.4740.21190.2460.1021-0.1921-0.40830.2447-0.0009-0.05370.09270.056-0.0201-19.1777-14.215-17.2498
22.75091.03041.52364.24842.03944.3893-0.12280.03510.4709-0.0419-0.0084-0.0982-0.21010.01220.13120.1062-0.0185-0.02750.02610.0270.0921-12.2547-5.77312.2848
31.89830.8462-0.53122.0621-1.2152.9038-0.0263-0.1797-0.01250.0956-0.06240.21740.0365-0.11570.08880.1096-0.03610.02330.10180.0067-0.0333-20.7065-25.69237.7668
42.14140.41220.4394.1960.35810.1082-0.0274-0.00490.2112-0.1037-0.08020.4953-0.4322-0.11610.10760.20060.0278-0.05420.0846-0.00690.0971-26.0989-7.4495-4.4285
54.53761.1784-0.72392.70741.26811.0554-0.0232-0.04360.2568-0.1822-0.03410.42710.1929-0.04160.05730.1701-0.0149-0.06440.105-0.01150.0264-28.4227-20.3701-9.0982
64.36633.00960.76264.43470.76511.25960.0636-0.41180.38420.397-0.15440.2291-0.1155-0.09040.09080.2013-0.00720.00580.1465-0.07180.0023-18.1152-10.461715.2453
74.6744-0.72330.33780.35850.02923.0197-0.1943-0.47810.05550.52580.10660.1837-0.37050.03580.08770.2718-0.01790.00890.1702-0.0033-0.0585-16.9911-20.519219.8071
84.54652.744-4.389910.7171.72796.35360.0885-0.7909-0.17650.2301-0.01650.1232-0.15221.3643-0.0720.1879-0.0673-0.06070.3036-0.0065-0.0464-6.2833-23.375417.1273
92.20281.6147-0.36835.7402-2.13146.15490.0894-0.02210.28250.1396-0.0592-0.4947-0.07590.2698-0.03020.065-0.0225-0.04560.0822-0.01580.06620.0894-12.8866-2.4736
102.62490.91590.33781.94631.12312.234-0.01920.1718-0.0755-0.1036-0.0210.07610.1969-0.11280.04020.1532-0.0509-0.02410.0729-0.0102-0.0492-15.6539-26.831-8.0049
111.61910.7695-1.20651.29680.14251.4494-0.1694-0.2799-0.302-0.05630.0116-0.26820.05160.36340.15780.1359-0.0119-0.01890.16570.04670.03581.4258-27.53082.3287
120.53891.01980.47863.12112.2827.5543-0.0811-0.2605-0.18960.20760.05830.02530.26130.33290.02280.15430.04130.01130.12840.08480.0307-8.7518-33.84448.3044
131.79970.4449-0.44083.0285-0.47890.9682-0.06580.2756-0.0077-0.37740.0351-0.33130.07830.04790.03070.1742-0.03690.02490.14440.0075-0.0252-3.0452-20.3385-15.469
143.3272-1.0698-0.41765.06031.41190.9334-0.21630.4321-0.0371-0.58790.1482-0.06050.01860.0070.06810.2372-0.0771-0.03190.1767-0.0166-0.0511-13.0258-22.5613-19.8205
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 94 - 11
2X-RAY DIFFRACTION2AA10 - 3312 - 35
3X-RAY DIFFRACTION3AA34 - 6736 - 69
4X-RAY DIFFRACTION4AA68 - 10770 - 109
5X-RAY DIFFRACTION5AA108 - 125110 - 127
6X-RAY DIFFRACTION6AA126 - 169128 - 171
7X-RAY DIFFRACTION7AA170 - 187172 - 189
8X-RAY DIFFRACTION8BB2 - 94 - 11
9X-RAY DIFFRACTION9BB10 - 2812 - 30
10X-RAY DIFFRACTION10BB29 - 6331 - 65
11X-RAY DIFFRACTION11BB64 - 10666 - 108
12X-RAY DIFFRACTION12BB107 - 126109 - 128
13X-RAY DIFFRACTION13BB127 - 169129 - 171
14X-RAY DIFFRACTION14BB170 - 187172 - 189

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