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- PDB-4lrf: Phosphopentomutase S154G variant soaked with ribose 5-phosphate -

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Basic information

Entry
Database: PDB / ID: 4lrf
TitlePhosphopentomutase S154G variant soaked with ribose 5-phosphate
ComponentsPhosphopentomutase
KeywordsISOMERASE / alkaline phosphatase family
Function / homology
Function and homology information


metabolic compound salvage / phosphopentomutase / phosphopentomutase activity / 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
5-O-phosphono-alpha-D-ribofuranose / : / Phosphopentomutase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / 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.mon_nstd_flag / _chem_comp.type / _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_alt_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_alt_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 2.2Nov 6, 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)140,65519
Polymers139,3513
Non-polymers1,30416
Water16,105894
1
A: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2228
Polymers46,4501
Non-polymers7727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8177
Polymers46,4501
Non-polymers3676
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6154
Polymers46,4501
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.922, 76.770, 107.530
Angle α, β, γ (deg.)90.00, 108.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphopentomutase / Phosphodeoxyribomutase


Mass: 46450.348 Da / Num. of mol.: 3 / Mutation: S154G
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.: 12 / 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-HSX / 5-O-phosphono-alpha-D-ribofuranose / 5-O-phosphono-alpha-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
IdentifierTypeProgram
a-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 894 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
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→50 Å / Num. obs: 94933 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Rsym value: 0.087 / Net I/σ(I): 17.2
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.386 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M8W

3m8w


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.013 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19984 4636 4.9 %RANDOM
Rwork0.16309 ---
obs0.16484 90127 99.85 %-
all-90265 --
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: 22.724 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å2-0 Å2-0.54 Å2
2---0.71 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9182 0 52 894 10128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199433
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1661.98912768
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54151184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57825.023438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.674151644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4871547
X-RAY DIFFRACTIONr_chiral_restr0.0770.21394
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217185
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_it0.2480.8364721
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.4381.2535910
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.4050.8944712
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→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 312 -
Rwork0.202 6594 -
obs--99.3 %
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)
12.2432-0.3318-0.34181.60160.34781.17740.03440.3222-0.0401-0.291-0.00180.1268-0.0201-0.0296-0.03270.1036-0.0004-0.00920.0495-0.00050.02011.86945.7087-14.4317
23.0332-0.13272.3080.2037-0.44082.3910.11850.2062-0.0169-0.0086-0.1539-0.07570.09370.45010.03540.11910.0163-0.0020.164-0.02380.155221.141918.44367.1625
33.0927-1.54511.31445.9265-2.53524.59410.1185-0.0941-0.09970.0334-0.14780.02850.1266-0.11780.02930.0235-0.0213-0.01590.1083-0.04320.069618.950115.617216.3289
40.9072-0.2231-0.2811.68330.23011.0127-0.0063-0.01940.0419-0.04260.01390.12990.0439-0.0591-0.00760.0262-0.003-00.00550.00130.0165-2.04688.9957-2.8403
52.3046-0.24042.6521.4422-0.26684.0987-0.1255-0.02590.133-0.13490.05860.1939-0.1398-0.32640.06680.0258-0.0072-0.0140.08720.0260.11-27.0183-0.994446.5664
61.08470.63440.06892.4346-0.00461.5386-0.0340.0936-0.0813-0.11340.06350.26150.0932-0.2306-0.02950.0193-0.0041-0.00770.06730.00910.1156-30.0627-5.134246.3349
74.3817-1.4779-0.30462.20140.97692.74230.06770.2960.0902-0.0031-0.09930.0280.0833-0.04210.03150.0866-0.01820.01180.08670.03560.0425-1.27084.156629.3146
80.96830.12230.47261.57590.09661.0401-0.0052-0.018-0.0092-0.00720.03940.0855-0.0071-0.0307-0.03410.0135-0.00160.02520.00230.00020.054-20.6069-3.938252.5576
91.3484-0.45421.10691.6434-1.51283.43180.05960.11840.0056-0.0342-0.2158-0.24030.26060.80720.15620.06170.0747-0.00090.32550.03920.116625.226-7.683862.1269
105.65821.1524-2.32445.1352-1.7212.75270.1726-0.91740.13290.0458-0.3722-0.6272-0.11390.9870.19970.16330.0237-0.00620.4705-0.00880.1212.1136-1.260284.9274
114.26030.7715-0.615.2562-0.17485.2834-0.0781-0.31780.0016-0.11370.0309-0.16460.07110.39970.04720.05890.06250.01690.1244-0.01440.045-4.3918-3.46478.4723
121.1415-0.50350.92271.5085-1.19653.5740.07750.10850.0112-0.1339-0.0962-0.03240.21770.5060.01880.05440.05740.01270.1715-0.00090.073616.811-5.272456.2095
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 DIFFRACTION5B3 - 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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