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- PDB-4lr9: Phosphopentomutase S154A variant soaked with 2,3-dideoxyribose 5-... -

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Basic information

Entry
Database: PDB / ID: 4lr9
TitlePhosphopentomutase S154A variant soaked with 2,3-dideoxyribose 5-phosphate
ComponentsPhosphopentomutase
KeywordsISOMERASE / alkaline phosphatase family
Function / homology
Function and homology information


phosphopentomutase / phosphopentomutase activity / cellular metabolic compound salvage / 2-deoxyribose 1-phosphate catabolic process / 5-phosphoribose 1-diphosphate biosynthetic process / nucleotide metabolic process / manganese ion binding / magnesium ion binding / cytosol
Similarity search - Function
Phosphopentomutase / Phosphopentomutase / Phosphopentomutase DeoB cap domain superfamily / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich ...Phosphopentomutase / Phosphopentomutase / Phosphopentomutase DeoB cap domain superfamily / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-dideoxy-5-O-phosphono-alpha-D-ribofuranose / : / Phosphopentomutase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBirmingham, W.A. / Starbird, C.A. / Panosian, T.D. / Nannemann, D.P. / Iverson, T.M. / Bachmann, B.O.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Bioretrosynthetic construction of a didanosine biosynthetic pathway.
Authors: Birmingham, W.R. / Starbird, C.A. / Panosian, T.D. / Nannemann, D.P. / Iverson, T.M. / Bachmann, B.O.
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Apr 30, 2014Group: Database references
Revision 1.4Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphopentomutase
B: Phosphopentomutase
C: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,32516
Polymers139,3933
Non-polymers93213
Water12,448691
1
A: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9196
Polymers46,4641
Non-polymers4555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7766
Polymers46,4641
Non-polymers3125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6294
Polymers46,4641
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.329, 76.615, 107.236
Angle α, β, γ (deg.)90.00, 108.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphopentomutase / Phosphodeoxyribomutase


Mass: 46464.375 Da / Num. of mol.: 3 / Mutation: S154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: BC_4087, deoB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q818Z9, phosphopentomutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-1X4 / 2,3-dideoxy-5-O-phosphono-alpha-D-ribofuranose / 2,3-dideoxyribose-5-phosphate / 2,3-dideoxy-5-O-phosphono-alpha-D-ribose / 2,3-dideoxy-5-O-phosphono-D-ribose / 2,3-dideoxy-5-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 198.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O6P
IdentifierTypeProgram
a-D-2,3-deoxy-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG3350, 50 mM manganese chloride, 50 mM ammonium acetate, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 81866 / % possible obs: 99 % / Observed criterion σ(F): -3 / Rsym value: 0.087 / Net I/σ(I): 17.5
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.37 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M8W

3m8w


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.928 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21267 4042 4.9 %RANDOM
Rwork0.1692 ---
obs0.17126 77794 98.85 %-
all-78597 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.648 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å2-0.37 Å2
2---1.19 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9193 0 34 691 9918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199363
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.21.98812665
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62651173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58425.023434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.199151630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1211546
X-RAY DIFFRACTIONr_chiral_restr0.080.21387
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217120
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4461.2964692
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7551.9415862
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7071.3844671
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 276 -
Rwork0.224 5361 -
obs--93.31 %
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)
11.7071-0.4724-0.42211.71120.61231.2011-0.01870.2836-0.0103-0.2393-0.00460.102-0.0166-0.00550.02320.09730.0009-0.00180.05880.01690.04741.92155.6663-14.3491
23.3234-0.23431.96140.2365-0.3722.04150.1066-0.0078-0.0348-0.0103-0.0757-0.1530.09960.3926-0.0310.14210.0107-0.00080.1857-0.03240.160221.136718.2047.0375
33.5359-1.40381.46116.4424-3.34055.26060.1289-0.2483-0.0945-0.0534-0.04770.14120.1551-0.126-0.08120.0485-0.015-0.02480.1541-0.04480.080619.042815.619516.35
41.0663-0.2598-0.40731.65590.15290.8785-0.0223-0.01790.031-0.01580.02270.13240.0321-0.043-0.00040.0615-0.004-0.01750.00470.0040.0317-2.07658.9253-2.8546
54.0056-1.18494.97862.2004-2.23028.8793-0.18620.0260.1544-0.0041-0.00860.1755-0.4177-0.23370.19480.03060.0226-0.0110.03-0.00760.1286-26.9469-0.777647.232
60.92840.6353-0.10322.67630.20581.6981-0.04510.1343-0.087-0.06270.10230.21520.1096-0.2131-0.05720.03360.0005-0.03780.0880.01940.1646-30.2188-4.989846.0997
74.8876-1.5512-0.14763.02450.94623.38170.05810.31990.13340.0561-0.1030.11760.1022-0.00650.04490.1003-0.0270.00170.0980.02340.0747-1.33094.258429.1818
81.02610.11150.41881.49370.01981.4479-0.0263-0.0173-0.00060.02310.03150.0696-0.0032-0.0186-0.00510.0226-0.00030.010.0014-0.00310.0817-20.7384-3.796652.3487
91.02-0.16981.29561.6979-1.78394.61080.08010.19290.0161-0.1195-0.3201-0.23830.4561.28350.240.08770.14850.00180.53390.05760.143325.3375-7.813162.0766
105.34991.4843-1.84674.1236-0.80982.31850.1226-0.7030.07090.0446-0.2162-0.5761-0.13950.71770.09360.1919-0.00520.00390.377-0.03080.12831.9745-1.397284.897
114.01521.0435-0.24225.71130.2585.2042-0.0788-0.0767-0.0617-0.13450.1749-0.2916-0.03190.3714-0.09620.06690.05270.02240.0963-0.02580.0768-4.3751-3.571178.2451
121.0272-0.52681.12241.4388-1.29144.79390.07890.13760.0122-0.1566-0.1471-0.02680.38030.7520.06820.07680.08090.00780.25160.02040.088416.8367-5.326456.2418
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 79
2X-RAY DIFFRACTION2A80 - 158
3X-RAY DIFFRACTION3A159 - 215
4X-RAY DIFFRACTION4A216 - 392
5X-RAY DIFFRACTION5B2 - 31
6X-RAY DIFFRACTION6B32 - 100
7X-RAY DIFFRACTION7B101 - 216
8X-RAY DIFFRACTION8B217 - 392
9X-RAY DIFFRACTION9C3 - 98
10X-RAY DIFFRACTION10C99 - 140
11X-RAY DIFFRACTION11C141 - 215
12X-RAY DIFFRACTION12C216 - 392

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