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- PDB-3tx0: Unphosphorylated Bacillus cereus phosphopentomutase in a P212121 ... -

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Basic information

Entry
Database: PDB / ID: 3tx0
TitleUnphosphorylated Bacillus cereus phosphopentomutase in a P212121 crystal form
ComponentsPhosphopentomutase
KeywordsISOMERASE / alkaline phosphatase superfamily
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
: / Phosphopentomutase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsPanosian, T.P. / Nanneman, D.P. / Bachmann, B.O. / Iverson, T.M.
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
DepositionSep 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6213
Polymers44,5111
Non-polymers1102
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.975, 75.706, 95.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphopentomutase / Phosphodeoxyribomutase


Mass: 44511.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: deoB, BC_4087 / Production host: Escherichia coli (E. coli) / References: UniProt: Q818Z9, phosphopentomutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 125 mM manganese chloride, 1.8 M ammonium citrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 225 mm CCD / Detector: CCD / Date: Apr 2, 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: 2.25→50 Å / Num. obs: 19421 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.25→2.33 Å / % possible all: 64.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 16.695 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24617 989 5.1 %RANDOM
Rwork0.18933 ---
all0.19212 19421 --
obs0.19212 18370 100 %-
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: 25.552 Å2
Baniso -1Baniso -2Baniso -3
1-4.78 Å20 Å20 Å2
2---6.8 Å20 Å2
3---2.02 Å2
Refinement stepCycle: LAST / Resolution: 2.26→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 2 27 3093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223126
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9844223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1885390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.88725.17147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26315558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4681515
X-RAY DIFFRACTIONr_chiral_restr0.0980.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212379
X-RAY DIFFRACTIONr_mcbond_it0.5491.51937
X-RAY DIFFRACTIONr_mcangle_it1.05123122
X-RAY DIFFRACTIONr_scbond_it1.95931189
X-RAY DIFFRACTIONr_scangle_it3.1714.51101
LS refinement shellResolution: 2.26→2.323 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 55 -
Rwork0.246 815 -
obs--100 %
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)
12.9721-0.7277-1.40382.62110.18962.8541-0.1162-0.25270.30250.66750.087-0.4228-0.0280.48410.02920.1780.0123-0.08630.243-0.05150.182113.7504-4.7935-18.8926
21.5195-0.15112.67390.1286-0.87118.5872-0.16230.42170.09930.0098-0.02430.0539-0.14050.4460.18660.0495-0.0490.03880.307-0.01440.25411.5542-15.6637-44.3915
35.1295-4.13484.26915.9903-5.279610.9911-0.5354-0.492-0.11340.58180.57860.526-0.3494-1.1639-0.04320.0951-0.00430.01020.33560.00790.1878-8.7002-15.973-46.8624
41.98440.4605-0.62983.95610.03251.8026-0.104-0.1320.08620.40840.0040.13920.1401-0.01080.10.0640.01350.03280.1596-0.02650.08291.6942-8.3981-19.946
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

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