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- PDB-3m8y: Phosphopentomutase from Bacillus cereus after glucose-1,6-bisphos... -

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Basic information

Entry
Database: PDB / ID: 3m8y
TitlePhosphopentomutase from Bacillus cereus after glucose-1,6-bisphosphate activation
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 / 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
ACETATE ION / : / Phosphopentomutase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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 1.2Jul 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 1.3Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_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 / _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

Downloads & links

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Assembly

Deposited unit
A: Phosphopentomutase
B: Phosphopentomutase
C: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,41526
Polymers133,7743
Non-polymers1,64123
Water13,601755
1
A: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,27310
Polymers44,5911
Non-polymers6819
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,20510
Polymers44,5911
Non-polymers6149
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9376
Polymers44,5911
Non-polymers3465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.153, 76.661, 107.758
Angle α, β, γ (deg.)90.00, 108.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 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 (bacteria) / Strain: ATCC 14579 / Gene: BC_4087, deoB / Plasmid: pET28(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q818Z9, phosphopentomutase

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Non-polymers , 5 types, 778 molecules

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


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.27 %

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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: 2.1→50 Å / Num. all: 82224 / Num. obs: 75463 / % possible obs: 91.8 % / Observed criterion σ(I): 2.5 / Redundancy: 3.6 % / Biso Wilson estimate: 16.5 Å2 / Rsym value: 0.084 / Net I/σ(I): 14.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 5869 / Rsym value: 0.257 / % possible all: 71.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0 / SU B: 8.536 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.198 5188 6.9 %RANDOM
Rwork0.1529 70183 --
obs0.1562 75371 91.79 %-
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: 96.05 Å2 / Biso mean: 32.2849 Å2 / Biso min: 10 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å2-0.76 Å2
2---1.51 Å20 Å2
3----0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9188 0 82 755 10025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229434
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.99212740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6551174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34625.103439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.904151661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.811546
X-RAY DIFFRACTIONr_chiral_restr0.0770.21384
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217150
X-RAY DIFFRACTIONr_mcbond_it0.3371.55832
X-RAY DIFFRACTIONr_mcangle_it0.66629383
X-RAY DIFFRACTIONr_scbond_it1.34333602
X-RAY DIFFRACTIONr_scangle_it2.2824.53354
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 231 -
Rwork0.179 4037 -
all-4268 -
obs--71.05 %
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)
12.059-0.3464-0.17591.87710.39551.5107-0.05130.3378-0.0113-0.34160.03750.09750.00470.03860.01390.1466-0.0065-0.01210.06780.01140.0362.21575.6152-14.648
23.2042-0.06392.55390.2238-0.3382.94090.18190.0497-0.12620.0226-0.0874-0.15660.060.4449-0.09450.1448-0.0257-0.00540.2044-0.04090.200620.784218.16137.0021
33.1333-0.9361.18464.9162-2.98045.18540.1494-0.2561-0.12960.1596-0.07790.06050.08580.0177-0.07150.1034-0.0405-0.03220.174-0.04370.102718.617615.495316.9426
41.2537-0.128-0.39991.78030.27951.1493-0.0046-0.03750.0337-0.01430.00420.1659-0.0026-0.06340.00040.0658-0.0014-0.01230.02280.00440.0381-2.07558.9112-2.5976
52.6821-0.82942.71631.932-0.94765.6181-0.03980.11380.1177-0.10940.00020.2732-0.0614-0.26520.03960.04-0.00590.01730.05650.01210.1189-27.6347-0.527946.1497
61.34761.172-0.05843.3504-0.08741.5113-0.03930.1666-0.0648-0.03880.10320.34670.08-0.2263-0.0640.02730.0023-0.01340.08090.01270.1476-30.3238-4.98846.2167
75.2022-1.7073-0.88891.95560.65032.57150.0810.41120.0003-0.0603-0.11290.0160.05750.01090.0320.0955-0.0144-0.00450.1120.02110.0598-1.51164.130229.6289
81.1370.140.34651.83480.01071.57490.0016-0.017-0.00470.02980.03640.08720.00230.0003-0.0380.0120.00050.02770.00110.00160.0651-20.4403-3.786352.6762
91.3415-0.35861.30511.9678-1.31393.49070.07750.0585-0.0341-0.0029-0.1561-0.26040.25670.79830.07860.07630.1033-0.00240.40940.04470.169724.8759-7.653362.3379
106.92163.2721-2.21763.2173-2.34365.17350.1738-1.1598-0.13470.1029-0.4494-0.6219-0.14181.35450.27570.1930.0090.02710.5951-0.0240.23331.4566-0.894985.4359
114.82541.007-1.44934.8149-0.86716.4752-0.1207-0.3056-0.1261-0.12010.01-0.19320.13960.55920.11060.06540.06810.02030.1434-0.02010.0631-4.6198-3.402578.3883
121.259-0.55711.09631.7087-0.96943.70180.07670.0637-0.0161-0.1103-0.0611-0.0240.28440.4789-0.01560.05880.06940.01130.21960.00430.12116.0287-5.293556.4214
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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