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- PDB-3uo0: phosphorylated Bacillus cereus phosphopentomutase soaked with glu... -

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Basic information

Entry
Database: PDB / ID: 3uo0
Titlephosphorylated Bacillus cereus phosphopentomutase soaked with glucose 1,6-bisphosphate
ComponentsPhosphopentomutase
KeywordsISOMERASE / alkaline phosphatase family
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: 2.3 Å
AuthorsIverson, T.M. / Birmingham, W.R. / Panosian, T.D. / Nannemann, D.P. / Bachmann, B.O.
CitationJournal: Biochemistry / Year: 2012
Title: Molecular Differences between a Mutase and a Phosphatase: Investigations of the Activation Step in Bacillus cereus Phosphopentomutase.
Authors: Iverson, T.M. / Panosian, T.D. / Birmingham, W.R. / Nannemann, D.P. / Bachmann, B.O.
History
DepositionNov 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...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 / 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.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

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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)134,67513
Polymers133,7743
Non-polymers90110
Water8,269459
1
A: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2176
Polymers44,5911
Non-polymers6265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7013
Polymers44,5911
Non-polymers1102
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)91.819, 77.075, 108.335
Angle α, β, γ (deg.)90.00, 108.94, 90.00
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) / Gene: deoB, BC_4087 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q818Z9, phosphopentomutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Sugar ChemComp-G16 / 1,6-di-O-phosphono-alpha-D-glucopyranose


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
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Enzyme was activated with 5 mM glucose 1,6-bisphosphate prior to crystallization over reservoir containing 100 mM Bis-Tris pH 5.5, 50 mM manganese chloride, 14% PEG3350, 50 mM ammonium ...Details: Enzyme was activated with 5 mM glucose 1,6-bisphosphate prior to crystallization over reservoir containing 100 mM Bis-Tris pH 5.5, 50 mM manganese chloride, 14% PEG3350, 50 mM ammonium acetate, crystals soaked in 5 mM glucose 1,6-bisphosphate prior to data collection, 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 / Date: Aug 21, 2010
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 63687 / Num. obs: 63499 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.38 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.722 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.216 7460 11.7 %RANDOM
Rwork0.18176 ---
obs0.18594 56040 99.7 %-
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 mean: 36.846 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å2-1.29 Å2
2---1.75 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9188 0 36 459 9683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0229351
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8891.9912651
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.42551168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44225.208432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.334151636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9561542
X-RAY DIFFRACTIONr_chiral_restr0.0520.21388
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217090
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_it0.0951.55805
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.18729349
X-RAY DIFFRACTIONr_scbond_it0.31133546
X-RAY DIFFRACTIONr_scangle_it0.5394.53302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 488 -
Rwork0.233 3999 -
obs--97.25 %
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)
11.8526-0.4641-0.46871.93790.45881.38310.00310.3303-0.0166-0.36320.00370.1037-0.0331-0.0273-0.00680.1595-0.0082-0.01390.07750.02220.04412.06255.7768-14.6583
22.86330.0422.21160.30350.01772.50680.12220.0356-0.1029-0.0129-0.0238-0.2060.06790.4443-0.09840.1676-0.03060.01590.2224-0.00880.189720.879818.29466.9831
33.5035-1.72591.3837.0245-3.85246.21380.1089-0.2363-0.07670.06010.04890.16280.10130.0081-0.15780.0819-0.0376-0.03110.1594-0.04710.123318.830415.656716.9656
41.0574-0.2581-0.32911.68590.30441.0299-0.0303-0.03370.0457-0.04360.03190.16960.0092-0.05-0.00160.0769-0.0054-0.00690.02340.0020.0528-2.00069.0168-2.718
52.8171-0.73742.9771.5433-0.785.7332-0.11470.10070.1668-0.0715-0.03340.2022-0.1417-0.2130.14810.0355-0.00450.02280.04360.0010.1542-27.5003-0.772146.9376
61.16030.8975-0.10453.0214-0.18771.2822-0.0350.1608-0.0408-0.08010.0840.31650.0675-0.2357-0.04910.0560.0008-0.03130.07820.00710.1623-30.3474-4.880246.4814
75.2319-1.9733-1.00232.30340.61242.91910.08730.4373-0.0202-0.0389-0.10150.06460.0313-0.0030.01420.1095-0.0212-0.01270.12120.01720.064-1.48944.130329.8316
80.99080.20760.39831.32930.04081.53730.0069-0.0305-0.0060.01060.02720.0937-0.0074-0.0202-0.03410.03280.00020.02610.0022-0.00160.0796-20.6476-3.866852.9481
91.1976-0.47831.37721.7192-1.47224.42020.07290.0891-0.0518-0.0646-0.1994-0.24170.36260.9640.12650.09590.12660.01240.48810.05760.174325.0093-7.687362.6811
107.70041.9209-2.47083.5564-1.91673.61180.1688-1.1270.06710.233-0.4517-0.829-0.16381.26540.28280.21940.02390.00630.59380.03560.251.6098-0.795385.7577
114.521.2334-1.55854.7725-1.16857.1335-0.0608-0.338-0.0153-0.0059-0.0314-0.17910.03330.63320.09220.09430.08130.02830.1593-0.0120.0662-4.5542-3.136578.9495
121.0921-0.571.03951.3805-1.09334.22390.08770.0849-0.0223-0.1772-0.0936-0.04770.37390.60550.00580.10060.08360.02160.25570.01280.122616.2785-5.271656.6305
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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