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- PDB-3ck2: Crystal structure of conserved uncharacterized protein (predicted... -

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Basic information

Entry
Database: PDB / ID: 3ck2
TitleCrystal structure of conserved uncharacterized protein (predicted phosphoesterase COG0622) from Streptococcus pneumoniae TIGR4
ComponentsConserved uncharacterized protein (predicted phosphoesterase COG0622)
KeywordsHYDROLASE / structural genomics / predicted phosphodiesterase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


retromer complex / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / retrograde transport, endosome to Golgi / protein transport / hydrolase activity / metal ion binding / cytosol
Similarity search - Function
YfcE-like, metallophosphatase domain / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / S,R MESO-TARTARIC ACID / Phosphoesterase / Phosphoesterase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsNocek, B. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of conserved uncharacterized protein (predicted phosphoesterase COG0622) from Streptococcus pneumoniae TIGR4.
Authors: Nocek, B. / Zhou, M. / Abdullah, J. / Joachimiak, A.
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved uncharacterized protein (predicted phosphoesterase COG0622)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6236
Polymers20,2921
Non-polymers3315
Water2,378132
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.467, 112.467, 112.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Conserved uncharacterized protein (predicted phosphoesterase COG0622)


Mass: 20292.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1879 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97NX4, UniProt: A0A0H2URP5*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0M K/Na Tartrate, Tris-HCl pH 7.0, 0.1M Lithium sulfate, 2mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2007 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 11690 / Num. obs: 10635 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 21.1 % / Rmerge(I) obs: 0.143 / Χ2: 1.524 / Net I/σ(I): 7.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 4.1 / Num. unique all: 484 / Χ2: 1.103 / % possible all: 92.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-2000data reduction
SHELXDphasing
HKL2Mapphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.88 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.201 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 507 4.8 %RANDOM
Rwork0.148 ---
all0.173 10635 --
obs0.15 10609 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.803 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 14 132 1553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221452
X-RAY DIFFRACTIONr_bond_other_d0.0020.02989
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9491963
X-RAY DIFFRACTIONr_angle_other_deg0.9732392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6665173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95123.64974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68615240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0681510
X-RAY DIFFRACTIONr_chiral_restr0.0890.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021623
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02316
X-RAY DIFFRACTIONr_nbd_refined0.180.2197
X-RAY DIFFRACTIONr_nbd_other0.2050.21047
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2665
X-RAY DIFFRACTIONr_nbtor_other0.0830.2753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.214
X-RAY DIFFRACTIONr_mcbond_it0.7561.51057
X-RAY DIFFRACTIONr_mcbond_other0.1621.5353
X-RAY DIFFRACTIONr_mcangle_it0.99121393
X-RAY DIFFRACTIONr_scbond_it1.7883679
X-RAY DIFFRACTIONr_scangle_it2.4734.5570
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 55 -
Rwork0.189 698 -
all-753 -
obs--99.34 %
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)
130.57669.06237.61316.05184.50473.3974-2.0481.43011.4116-1.36681.8899-0.2669-1.28091.05890.15810.3073-0.22660.02960.63820.17730.430424.3701-3.3813-22.0288
23.5250.129-1.02694.3997-0.15714.9234-0.01630.4362-0.1613-0.3939-0.0662-0.18370.34970.05060.08250.05820.0688-0.0110.09320.02310.03439.596-19.216-20.3404
36.77371.53-2.5425.6684-2.04313.7492-0.12180.0175-0.0552-0.1301-0.1289-0.17740.32910.39460.2507-0.00060.0837-0.05010.08050.05880.024912.4728-18.9603-14.8445
43.8461.6162-1.81064.901-1.66322.5736-0.0608-0.0279-0.2318-0.3097-0.1713-0.46820.16120.40970.23210.04080.1286-0.03230.10260.05610.073214.0116-23.499-11.9402
53.64852.2108-0.65974.3139-3.60293.56890.0556-0.2118-0.0410.0789-0.277-0.26020.03770.1510.22140.15480.0511-0.00510.17380.02470.110512.321-21.8939-3.9937
63.62491.1299-1.87333.9831-1.78096.2913-0.081-0.22740.19980.3435-0.2141-0.6079-0.21890.70680.29510.073-0.0265-0.13130.05390.07460.121515.8492-10.3134-5.6834
726.44668.1564-5.12146.8555-1.70398.31990.2235-1.51441.1770.6726-0.3120.0307-1.04790.52940.08850.3079-0.0913-0.11420.0599-0.03940.058911.6181-3.94991.6439
82.2189-0.6395-1.85792.1682-1.54543.73830.0634-0.19790.4420.4081-0.1849-0.1303-0.29620.3230.12150.1145-0.0076-0.080.11250.03610.089210.6588-7.5744-7.6153
922.13068.052124.50462.92978.915927.1334-0.064-1.54360.93481.6842-0.96550.2119-1.0305-0.96961.02950.3752-0.0185-0.02930.26570.00620.354810.03481.5226-8.8281
102.44560.4586-0.04753.5062-0.11675.1158-0.06390.44180.54630.08460.0170.0407-0.30210.46410.04690.03540.0378-0.04040.07240.07270.11667.4327-7.9934-11.9964
1116.2388-8.8361-8.75416.83996.07537.0107-0.1533-0.61030.26610.42480.26890.3790.1302-0.19-0.11560.06180.02210.01940.13680.06150.0791-4.7682-9.1891-16.0884
129.3362.67971.59133.5821.3312.3096-0.12580.6060.4646-0.19140.0146-0.2879-0.17930.34620.11120.0376-0.0105-0.01450.14620.14370.126813.0458-3.4648-20.6266
131.6962.16611.573622.33671.97591.58670.06590.2037-0.12-0.8986-0.1920.4796-0.00540.10680.12620.06370.0305-0.0110.18550.04970.06552.7275-9.9766-26.2967
1422.03083.03544.84592.75992.18992.98910.7257-0.07060.60450.2662-0.5869-0.6738-0.37520.3088-0.13880.1176-0.0756-0.04760.06820.05650.186111.2543.0067-17.9051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 53 - 8
2X-RAY DIFFRACTION2AA6 - 289 - 31
3X-RAY DIFFRACTION3AA29 - 4232 - 45
4X-RAY DIFFRACTION4AA43 - 5746 - 60
5X-RAY DIFFRACTION5AA58 - 6961 - 72
6X-RAY DIFFRACTION6AA70 - 8773 - 90
7X-RAY DIFFRACTION7AA88 - 10091 - 103
8X-RAY DIFFRACTION8AA101 - 114104 - 117
9X-RAY DIFFRACTION9AA115 - 120118 - 123
10X-RAY DIFFRACTION10AA121 - 133124 - 136
11X-RAY DIFFRACTION11AA134 - 140137 - 143
12X-RAY DIFFRACTION12AA141 - 158144 - 161
13X-RAY DIFFRACTION13AA159 - 165162 - 168
14X-RAY DIFFRACTION14AA166 - 173169 - 176

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