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- PDB-3m8w: Phosphopentomutase from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 3m8w
TitlePhosphopentomutase from Bacillus cereus
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 / : / Phosphopentomutase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 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

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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)134,74518
Polymers133,7743
Non-polymers97115
Water17,078948
1
A: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0558
Polymers44,5911
Non-polymers4647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9336
Polymers44,5911
Non-polymers3425
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)91.238, 76.552, 106.561
Angle α, β, γ (deg.)90.000, 108.890, 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 / References: UniProt: Q818Z9, phosphopentomutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 948 / 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: 2.66 Å3/Da / Density % sol: 53.74 %

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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: 1.85→45.7 Å / Num. obs: 116902 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5 / Redundancy: 3.1 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.08 / Net I/σ(I): 13.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3 / Num. unique all: 11723 / Rsym value: 0.369 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementResolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.924 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1857 5847 5 %RANDOM
Rwork0.1568 110953 --
obs0.1582 116800 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 max: 78.7 Å2 / Biso mean: 31.2195 Å2 / Biso min: 14.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å2-1.27 Å2
2---1.04 Å20 Å2
3----1.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9196 0 38 948 10182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229404
X-RAY DIFFRACTIONr_angle_refined_deg1.081.98812721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44151179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47925.069436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.589151646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0051546
X-RAY DIFFRACTIONr_chiral_restr0.0730.21387
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217166
X-RAY DIFFRACTIONr_mcbond_it0.3461.55853
X-RAY DIFFRACTIONr_mcangle_it0.67429424
X-RAY DIFFRACTIONr_scbond_it1.23833551
X-RAY DIFFRACTIONr_scangle_it2.1274.53297
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 454 -
Rwork0.209 8135 -
all-8589 -
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)
10.9467-0.152-0.09121.19540.19540.69360.01370.1556-0.0232-0.2489-0.00830.07550.00130.0026-0.00540.0790.0003-0.0050.04750.00690.02551.80995.5726-14.281
21.50810.10330.64450.6975-0.32381.82650.0753-0.0461-0.0150.0506-0.0503-0.18220.01950.303-0.0250.0371-0.0047-0.00460.0836-0.02910.094720.996318.16366.6571
32.0836-0.8670.6484.7062-2.31263.80710.1377-0.1677-0.07150.1031-0.08850.05360.08520.0456-0.04930.0336-0.0233-0.03140.1253-0.02160.073218.53515.446416.4699
40.4269-0.0681-0.01411.02740.06030.5267-0.0202-0.0030.0144-0.0270.01090.08810.021-0.02560.00940.0375-0.00140.00290.04570.00530.0595-2.05589.008-2.4164
51.2945-0.08660.97430.7794-0.28852.3715-0.0677-0.02260.0697-0.05810.02690.1267-0.0575-0.19060.04080.01080.0073-0.01730.0367-0.00210.1029-26.9795-0.48647.1167
60.82760.4448-0.0621.61990.03881.0548-0.02510.07-0.0435-0.06690.04660.20630.0294-0.1575-0.02150.0047-0.0005-0.01090.07560.00890.1163-30.1282-4.986145.73
73.1286-1.20230.10381.4390.16391.91750.04110.33750.1619-0.01-0.1059-0.0520.070.06290.06480.0258-0.00810.01070.07640.03320.0234-1.38033.723129.2392
80.48950.01220.12160.7771-0.03050.65290.0063-0.0039-0.0125-0.00380.01570.06420.0113-0.021-0.0220.02390.00030.01680.0432-0.00010.0781-20.1577-3.688852.1388
90.8406-0.40560.83691.1743-1.15642.84930.0760.12420.0262-0.0173-0.1982-0.21240.34320.88140.12210.06480.1385-0.01670.37380.04080.088725.0966-7.643861.6572
104.85991.0042-1.98833.3075-1.01662.48080.0286-0.8376-0.03030.1037-0.1557-0.3335-0.03480.79880.1270.08160.0242-0.02140.3485-0.01880.05712.2111-1.879384.3513
112.58850.1974-0.7672.79380.09924.2267-0.1144-0.2182-0.0335-0.00540.0907-0.06740.13810.33550.02370.02430.04360.0150.1087-0.01110.0597-4.2955-3.513677.3731
120.7678-0.29170.58071.0033-0.68723.24270.07780.07290.0348-0.0909-0.1002-0.06910.33120.59770.02240.04340.08050.00260.17220.0170.041816.4581-5.162955.8223
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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