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- PDB-3m8z: Phosphopentomutase from Bacillus cereus bound with ribose-5-phosphate -

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Basic information

Entry
Database: PDB / ID: 3m8z
TitlePhosphopentomutase from Bacillus cereus bound with ribose-5-phosphate
ComponentsPhosphopentomutase
KeywordsISOMERASE / alkaline phosphatase like core domain / di-metallo catalytic center / manganese binding / manganese / metal-binding
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
ACETATE ION / 5-O-phosphono-alpha-D-ribofuranose / : / Phosphopentomutase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsPanosian, T.D. / Nannemann, D.P. / Watkins, G. / 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
DepositionMar 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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)135,21619
Polymers133,7743
Non-polymers1,44216
Water17,655980
1
A: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4909
Polymers44,5911
Non-polymers8988
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9706
Polymers44,5911
Non-polymers3795
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)91.588, 76.755, 107.083
Angle α, β, γ (deg.)90.00, 108.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 5 molecules ABC

#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 (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: deoB, BC_4087 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q818Z9, phosphopentomutase
#6: 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

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Non-polymers , 5 types, 994 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 980 / 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→46.01 Å / Num. all: 130328 / Num. obs: 128719 / % possible obs: 98.8 % / Observed criterion σ(I): 2.5 / Redundancy: 3.6 % / Biso Wilson estimate: 19 Å2 / Rsym value: 0.063 / Net I/σ(I): 25.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 11750 / Rsym value: 0.38 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementStarting model: PDB ENTRY 3M8W

3m8w


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.97 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 6127 4.8 %RANDOM
Rwork0.1683 122526 --
obs0.1697 128653 98.82 %-
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: 78.69 Å2 / Biso mean: 27.0423 Å2 / Biso min: 11.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å2-0.98 Å2
2---1.18 Å20 Å2
3----0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9195 0 69 980 10244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229504
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.99212858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39851188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61425.011441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14151675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4331548
X-RAY DIFFRACTIONr_chiral_restr0.0740.21401
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217214
X-RAY DIFFRACTIONr_mcbond_it0.3581.55871
X-RAY DIFFRACTIONr_mcangle_it0.70729467
X-RAY DIFFRACTIONr_scbond_it1.31933633
X-RAY DIFFRACTIONr_scangle_it2.2834.53391
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 394 -
Rwork0.247 8038 -
all-8432 -
obs--88.69 %
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)
11.7938-0.1099-0.26391.18660.18161.12430.01170.2516-0.0031-0.2392-0.00310.0888-0.0014-0.0104-0.00860.09690.003-0.00480.0490.01090.0251.55335.8086-14.4979
21.8543-0.13521.29190.1379-0.26841.1990.07720.0701-0.00990.0066-0.112-0.08860.04290.26730.03480.14880.0114-0.0110.1794-0.01990.164321.310918.24076.7452
31.731-0.47020.24193.7646-1.7462.73940.0764-0.1677-0.06220.08480.0080.09240.0469-0.0816-0.08440.0572-0.015-0.0270.1242-0.03250.088618.792615.548216.3949
41.2115-0.1295-0.26141.49980.14551.0506-0.0286-0.04690.03220.02060.01670.10720.0137-0.0440.01190.0274-0.0056-0.0040.00670.00120.0183-2.18559.1879-2.3342
52.1861-0.44221.56391.0465-0.53753.8125-0.00180.0670.083-0.05340.02460.154-0.1101-0.2618-0.02290.02240.0042-0.00110.0441-0.00060.0939-27.2637-0.631946.2664
61.03030.62360.10561.92620.08781.1187-0.03060.1114-0.0462-0.06120.07560.22690.0503-0.202-0.04510.01920.0072-0.00260.08490.00580.111-30.1087-5.001846.1602
73.0541-0.974-0.29991.62370.46361.83990.0150.20030.0628-0.0257-0.04850.00470.06150.01280.03350.0969-0.01960.00470.10660.02450.0692-1.27173.829529.4533
80.99380.09310.28831.40280.01441.5071-0.0022-0.01950.00340.0280.01890.0243-0.02820.0138-0.01670.00680.00170.0180.00140.00490.0524-19.9049-3.42552.6651
90.7462-0.09820.34511.0819-0.38051.44060.00320.0155-0.02760.0192-0.0594-0.21720.15910.35260.05620.10510.0464-0.01510.28040.02850.162325.407-7.813562.1144
102.75410.9595-0.3741.9736-0.57860.68860.0231-0.37750.0210.114-0.1217-0.3074-0.03480.30050.09870.1990.0155-0.00690.2891-0.0110.16272.3153-1.538785.1397
112.85830.5178-0.12143.0223-0.05872.955-0.0925-0.0885-0.0327-0.0560.0726-0.12420.01260.18410.01990.08240.04840.01590.1092-0.00810.0762-3.9524-3.420278.0331
120.7927-0.13650.34631.0301-0.41532.10190.02510.03820.0191-0.0626-0.0321-0.03840.1540.27270.0070.07860.04120.0010.16490.01060.106116.5072-5.102856.1471
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2water_rep.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3ion.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4ligands.par&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_TOPOLOGY_INFILE_5

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