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- PDB-4r7o: Crystal Structure of Putative Glycerophosphoryl Diester Phosphodi... -

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Basic information

Entry
Database: PDB / ID: 4r7o
TitleCrystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus anthraci
ComponentsGlycerophosphoryl diester phosphodiesterase, putativeGlycerophosphodiester phosphodiesterase
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-structure / TIM barrel
Function / homology
Function and homology information


glycerophosphodiester phosphodiesterase activity / phospholipid catabolic process / metal ion binding
Similarity search - Function
Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Phosphatidylinositol (PI) phosphodiesterase / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Glycerophosphodiester phosphodiesterase / Putative glycerophosphoryl diester phosphodiesterase
Similarity search - Component
Biological speciesBacillus anthracis str. Ames (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.534 Å
AuthorsKim, Y. / Zhou, M. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus anthraci
Authors: Kim, Y. / Zhou, M. / Shatsman, S. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: Glycerophosphoryl diester phosphodiesterase, putative
B: Glycerophosphoryl diester phosphodiesterase, putative
C: Glycerophosphoryl diester phosphodiesterase, putative
D: Glycerophosphoryl diester phosphodiesterase, putative
E: Glycerophosphoryl diester phosphodiesterase, putative
F: Glycerophosphoryl diester phosphodiesterase, putative
G: Glycerophosphoryl diester phosphodiesterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,59134
Polymers235,6017
Non-polymers1,99027
Water11,710650
1
A: Glycerophosphoryl diester phosphodiesterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2208
Polymers33,6571
Non-polymers5637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycerophosphoryl diester phosphodiesterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9665
Polymers33,6571
Non-polymers3094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glycerophosphoryl diester phosphodiesterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9805
Polymers33,6571
Non-polymers3234
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glycerophosphoryl diester phosphodiesterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9665
Polymers33,6571
Non-polymers3094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Glycerophosphoryl diester phosphodiesterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0006
Polymers33,6571
Non-polymers3435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Glycerophosphoryl diester phosphodiesterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6822
Polymers33,6571
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Glycerophosphoryl diester phosphodiesterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7783
Polymers33,6571
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)209.644, 85.891, 191.539
Angle α, β, γ (deg.)90.00, 121.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 7 molecules ABCDEFG

#1: Protein
Glycerophosphoryl diester phosphodiesterase, putative / Glycerophosphodiester phosphodiesterase / Putative glycerophosphoryl diester phosphodiesterase


Mass: 33657.344 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. Ames (bacteria)
Strain: Ames / Gene: BA_3560, BAS3300, GBAA_3560 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q81YI6, UniProt: A0A6L7H2E6*PLUS

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Non-polymers , 6 types, 677 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M litium sulfate, 0.1 M Tris pH 8.5, 30 %(w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 95660 / Num. obs: 95660 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 33.28 Å2 / Rsym value: 0.137 / Net I/σ(I): 22.4
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 4633 / Rsym value: 0.678 / % possible all: 97.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIXmodel building
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2p76

2p76


Resolution: 2.534→37.696 Å / SU ML: 0.29 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1965 2.09 %random
Rwork0.154 ---
all0.155 93834 --
obs0.155 93834 96.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.2 Å2
Refinement stepCycle: LAST / Resolution: 2.534→37.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15688 0 110 650 16448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816172
X-RAY DIFFRACTIONf_angle_d1.07721809
X-RAY DIFFRACTIONf_dihedral_angle_d14.5466190
X-RAY DIFFRACTIONf_chiral_restr0.0432327
X-RAY DIFFRACTIONf_plane_restr0.0052782
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5343-2.59770.30831260.23285791591786
2.5977-2.66790.26841440.21766214635893
2.6679-2.74640.26961240.20276385650995
2.7464-2.8350.27621440.19926426657095
2.835-2.93630.26781310.19366501663296
2.9363-3.05380.24411430.18746543668697
3.0538-3.19270.22221400.18816640678098
3.1927-3.36090.21831380.17276652679099
3.3609-3.57140.22381480.15636717686599
3.5714-3.84690.17581480.1326710685899
3.8469-4.23350.16931400.116567526892100
4.2335-4.8450.15591460.105467816927100
4.845-6.10010.15281400.128668356975100
6.1001-37.70020.18061530.14926922707599
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)
12.13490.34750.05372.1847-0.1322.46-0.0473-0.25230.170.1484-0.00190.07-0.2050.02670.04770.24380.0597-0.02760.29790.03970.252265.370723.246340.2161
24.6208-0.26032.27553.4335-2.7633.86770.02620.4547-0.0036-0.246-0.2431-0.45430.010.61980.12720.20020.01810.03930.2608-0.01160.280272.057428.657424.3553
32.0169-0.34130.091.9144-0.26091.71170.02880.0404-0.0744-0.07020.03230.09510.0233-0.0461-0.0560.17640.0171-0.00730.17160.00590.212952.12521.058822.0365
41.9767-0.1591-0.32731.92160.40133.45450.01480.0351-0.08680.0920.03790.13370.2751-0.1449-0.04330.23880.0478-0.03060.27040.01620.2781-22.892644.846248.6203
52.1392-0.27620.28761.9140.46453.2831-0.0191-0.0261-0.07150.06280.0132-0.14230.10060.09370.00510.1528-0.0154-0.02920.14670.02850.1899-1.958345.703549.4148
62.3095-0.55030.23712.9567-0.41562.34-0.02120.0332-0.0909-0.0379-0.0040.27780.0221-0.16690.02230.20080.0195-0.04310.249-0.02190.212925.693216.3374-20.9779
71.11410.3790.3891.56810.47192.3472-0.051-0.02160.00290.083-0.0070.085-0.0469-0.01570.0560.16030.032-0.01560.1890.0130.223235.741120.6111-5.4095
83.52680.0635-0.58673.6239-0.98073.58710.03070.03330.0165-0.0032-0.0794-0.2583-0.10210.59650.03350.23370.006-0.04660.2586-0.03140.208713.87742.895975.0706
91.2548-0.40871.22133.6251-1.45717.55740.09850.0452-0.1178-0.13820.14060.4765-0.6408-0.3643-0.09290.29160.02710.01260.1828-0.00830.3521.587653.24879.7286
101.5096-0.10660.00312.5750.10094.0891-0.0233-0.30840.04080.22240.0901-0.04260.13460.2306-0.0530.18560.0384-0.00570.2220.00510.22596.994840.280895.8891
112.9887-0.3234-0.20682.07630.13811.62320.1304-0.06720.27050.0452-0.02480.0233-0.24280.0486-0.09440.22470.00270.03730.15840.02590.232242.875352.031422.5358
122.1462-0.2799-1.02581.2739-0.00512.38870.1754-0.0570.22420.04860.0027-0.0134-0.1855-0.0942-0.13970.19180.03050.01180.17080.00370.341826.570352.397832.7989
131.31340.5031-2.65122.9033-0.66779.50320.13370.05930.11190.0343-0.18490.04210.19530.20470.08980.19730.05180.06040.25140.01610.282822.912717.559833.202
142.5268-0.65580.37451.64310.1743.2416-0.03880.3257-0.1343-0.0904-0.01720.18110.1826-0.24010.0510.2914-0.05350.04150.29510.02920.304425.252814.413621.507
153.69430.8965-0.72118.26532.49196.11970.06010.4858-0.2560.2037-0.15940.30810.9591-0.39320.05740.43850.0471-0.00520.2335-0.03720.326627.30964.060130.847
167.1198-0.1027-2.83921.4993-0.76752.2453-0.34590.1286-0.27580.1296-0.0177-0.20790.61740.04330.32310.490.02230.07310.187-0.01150.312929.1668-0.555335.4813
173.80330.0346-0.52234.6136-0.75923.1307-0.04580.1282-0.1542-0.3063-0.01610.18560.4845-0.58680.05010.3425-0.09830.0210.3105-0.00010.201510.0084.334544.3071
181.85130.4358-0.66334.0964-0.29671.51880.2089-0.27610.22150.0717-0.16420.074-0.10240.0047-0.0230.31560.00260.03650.2593-0.02220.291517.556221.205744.1819
193.29590.9411-0.31212.8429-0.03575.44160.2981-0.77410.05460.3769-0.2015-0.3032-0.1860.1874-0.12920.39850.01690.04970.67090.0720.424538.800218.63478.8643
203.3620.3992-0.21223.46520.44984.70570.0269-0.1341-0.42470.1387-0.0627-0.170.9392-0.1890.08240.51460.00730.04880.42360.06680.38241.3194.006166.13
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 161 )
2X-RAY DIFFRACTION2chain 'A' and (resid 162 through 201 )
3X-RAY DIFFRACTION3chain 'A' and (resid 202 through 313 )
4X-RAY DIFFRACTION4chain 'B' and (resid 35 through 184 )
5X-RAY DIFFRACTION5chain 'B' and (resid 185 through 313 )
6X-RAY DIFFRACTION6chain 'C' and (resid 34 through 161 )
7X-RAY DIFFRACTION7chain 'C' and (resid 162 through 313 )
8X-RAY DIFFRACTION8chain 'D' and (resid 35 through 161 )
9X-RAY DIFFRACTION9chain 'D' and (resid 162 through 191 )
10X-RAY DIFFRACTION10chain 'D' and (resid 192 through 313 )
11X-RAY DIFFRACTION11chain 'E' and (resid 34 through 161 )
12X-RAY DIFFRACTION12chain 'E' and (resid 162 through 313 )
13X-RAY DIFFRACTION13chain 'F' and (resid 37 through 54 )
14X-RAY DIFFRACTION14chain 'F' and (resid 55 through 143 )
15X-RAY DIFFRACTION15chain 'F' and (resid 144 through 161 )
16X-RAY DIFFRACTION16chain 'F' and (resid 162 through 211 )
17X-RAY DIFFRACTION17chain 'F' and (resid 212 through 284 )
18X-RAY DIFFRACTION18chain 'F' and (resid 285 through 313 )
19X-RAY DIFFRACTION19chain 'G' and (resid 35 through 161 )
20X-RAY DIFFRACTION20chain 'G' and (resid 162 through 313 )

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