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- PDB-3ot9: Phosphopentomutase from Bacillus cereus bound to glucose-1,6-bisp... -

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Basic information

Entry
Database: PDB / ID: 3ot9
TitlePhosphopentomutase from Bacillus cereus bound to glucose-1,6-bisphosphate
ComponentsPhosphopentomutase
KeywordsISOMERASE / alkaline phosphatase like core domain / phosphopentomutase / ribose-5-phosphate / ribose-1-phosphate / glucose-1 / 6-bisphosphate / phosphoryl transfer
Function / homology
Function and homology information


phosphopentomutase / phosphopentomutase activity / cellular metabolic compound salvage / 5-phosphoribose 1-diphosphate biosynthetic process / deoxyribonucleotide catabolic 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
1,6-di-O-phosphono-alpha-D-glucopyranose / : / Phosphopentomutase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPanosian, T.D. / Nannemann, D.P. / Watkins, G. / Phalen, V. / Wadzinski, B. / Bachmann, B.O. / Iverson, T.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Bacillus cereus Phosphopentomutase Is an Alkaline Phosphatase Family Member That Exhibits an Altered Entry Point into the Catalytic Cycle.
Authors: Panosian, T.D. / Nannemann, D.P. / Watkins, G.R. / Phelan, V.V. / McDonald, W.H. / Wadzinski, B.E. / Bachmann, B.O. / Iverson, T.M.
History
DepositionSep 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _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.pdbx_leaving_atom_flag / _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 1.3Sep 6, 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

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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)134,88416
Polymers133,7743
Non-polymers1,11013
Water19,7261095
1
A: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2797
Polymers44,5911
Non-polymers6886
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8485
Polymers44,5911
Non-polymers2574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7564
Polymers44,5911
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.871, 76.582, 107.051
Angle α, β, γ (deg.)90.000, 108.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphopentomutase / / Phosphodeoxyribomutase


Mass: 44591.305 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: BC_4087, deoB / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 gold DE3 / References: UniProt: Q818Z9, phosphopentomutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-G16 / 1,6-di-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE / 1,6-di-O-phosphono-alpha-D-glucose / 1,6-di-O-phosphono-D-glucose / 1,6-di-O-phosphono-glucose / Glucose 1,6-bisphosphate


Type: D-saccharide / Mass: 339.108 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O12P2
IdentifierTypeProgram
a-D-Glcp1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1095 / 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: 2.67 Å3/Da / Density % sol: 53.86 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 141561 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.053 / Net I/σ(I): 23.7
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.298 / % possible all: 69.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M8W
Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.436 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 6361 4.8 %RANDOM
Rwork0.1623 ---
obs0.1636 126882 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 113.66 Å2 / Biso mean: 26.9567 Å2 / Biso min: 8.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å2-0.64 Å2
2---0.99 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9188 0 47 1095 10330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229459
X-RAY DIFFRACTIONr_angle_refined_deg1.0761.99112793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.40851184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4825.124443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.031151683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9811546
X-RAY DIFFRACTIONr_chiral_restr0.0730.21396
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217172
X-RAY DIFFRACTIONr_mcbond_it0.311.55825
X-RAY DIFFRACTIONr_mcangle_it0.61129398
X-RAY DIFFRACTIONr_scbond_it1.18533634
X-RAY DIFFRACTIONr_scangle_it2.0174.53387
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 341 -
Rwork0.263 6430 -
all-6771 -
obs--66.17 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.599-0.2397-0.38611.84670.32281.5384-0.01020.3399-0.034-0.33090.00720.1055-0.0046-0.00840.00290.120.0002-0.01990.05370.00840.02661.4645.801-14.514
23.8571-0.35072.24940.5076-0.58162.6760.08460.02260.0701-0.0157-0.1003-0.24440.0110.52010.01570.0947-0.00650.00150.1943-0.0380.16521.2518.146.689
32.9112-0.96060.66065.9452-3.5765.49560.0992-0.2611-0.06710.098-0.04470.11830.0236-0.0166-0.05450.051-0.0164-0.0360.1741-0.04640.072118.78815.56716.397
41.4925-0.1397-0.31671.93530.18771.1152-0.0324-0.04820.03610.00410.02190.1606-0.0013-0.03470.01050.0342-0.0047-0.00280.00490.00090.0289-2.29.231-2.323
52.9553-0.47092.42121.1585-0.8856.143-0.05510.08110.101-0.07480.05450.205-0.2017-0.30080.00060.02460.005-0.00920.03970.00150.0958-27.205-0.67246.369
61.41151.0092-0.02482.87530.00721.4918-0.03430.1359-0.077-0.06750.07470.31630.0918-0.266-0.04040.02450.0043-0.010.09390.00520.1211-30.2-5.06246.255
75.2697-2.0141-0.30022.25420.5982.91080.05940.39420.1294-0.0149-0.1155-0.00010.09880.07150.05610.0945-0.01640.00770.10630.03720.0666-1.2793.74629.451
81.11940.15990.36641.7371-0.0531.7902-0.0007-0.0312-0.01370.04870.02960.0469-0.00830.0004-0.0290.01040.00010.02150.00220.00120.0549-19.983-3.40952.746
91.4004-0.53481.37761.8945-1.48245.13630.1260.18610.0129-0.0576-0.3043-0.26290.64261.43990.17820.13190.2052-0.00730.60690.07630.161525.389-7.79762.096
105.89090.9042-2.10782.9002-1.42263.21050.1098-0.9870.06940.1839-0.2627-0.5059-0.15690.9720.15290.1853-0.0065-0.02710.4693-0.02370.15122.274-1.51285.139
114.47930.2695-0.75594.35760.03845.6934-0.0996-0.2484-0.0256-0.05960.1031-0.1963-0.00630.4871-0.00350.04980.0440.01410.1291-0.01650.0592-3.995-3.40878.022
121.1367-0.42320.88381.6153-1.26265.40180.12020.08860.0281-0.1322-0.1705-0.03550.49260.85560.05030.10110.1077-0.00020.27840.02230.097716.536-5.11456.196
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 - 393
9X-RAY DIFFRACTION9C3 - 98
10X-RAY DIFFRACTION10C99 - 140
11X-RAY DIFFRACTION11C141 - 215
12X-RAY DIFFRACTION12C216 - 392

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