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- PDB-3ddh: The structure of a putative haloacid dehalogenase-like family hyd... -

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Basic information

Entry
Database: PDB / ID: 3ddh
TitleThe structure of a putative haloacid dehalogenase-like family hydrolase from Bacteroides thetaiotaomicron VPI-5482
ComponentsPutative haloacid dehalogenase-like family hydrolase
KeywordsHYDROLASE / HAD superfamily / Bacteroides thetaiotaomicron / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle ...Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative haloacid dehalogenase-like family hydrolase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsCuff, M.E. / Duggan, E. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a putative haloacid dehalogenase-like family hydrolase from Bacteroides thetaiotaomicron VPI-5482
Authors: Cuff, M.E. / Duggan, E. / Abdullah, J. / Joachimiak, A.
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 16, 2014Group: Experimental preparation
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative haloacid dehalogenase-like family hydrolase
B: Putative haloacid dehalogenase-like family hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,74410
Polymers53,3922
Non-polymers3528
Water6,161342
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-73 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.119, 104.222, 121.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe dimer in the AU is likely to be relevant.

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Components

#1: Protein Putative haloacid dehalogenase-like family hydrolase


Mass: 26695.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_2180 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8A5Q8
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M MgCl2, 0.1M HEPES pH7, 25% PEG 3350, 3% D(+) Trehalose dihydrate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97855 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 8, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionRedundancy: 8.8 % / Av σ(I) over netI: 7.2 / Number: 280444 / Rmerge(I) obs: 0.108 / Χ2: 1.73 / D res high: 2 Å / D res low: 50 Å / Num. obs: 31723 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.935097.310.0876.6418.1
3.914.9310010.0723.628.3
3.423.9110010.0772.6888.9
3.113.4210010.0882.0949.2
2.883.1110010.1111.649.4
2.712.8810010.1321.3129.5
2.582.7199.910.1491.0889.6
2.472.5810010.1780.9989.5
2.372.4799.810.1980.879.6
2.292.3710010.2120.829.6
2.222.2999.710.2690.8119.4
2.152.2210010.2920.7539.1
2.12.1599.510.3560.7418.6
2.052.199.510.4090.8717.7
22.059310.4431.0385.9
ReflectionResolution: 2→50 Å / Num. all: 31723 / Num. obs: 31723 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.108 / Χ2: 1.729 / Net I/σ(I): 7.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3 / Num. unique all: 1939 / Χ2: 1.038 / % possible all: 93

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2 Å / D res low: 50 Å / FOM : 0.254 / FOM acentric: 0.29 / FOM centric: 0 / Reflection: 31605 / Reflection acentric: 27721 / Reflection centric: 3884
Phasing MAD setR cullis acentric: 2.02 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 50 Å / Loc acentric: 0.2 / Loc centric: 0.2 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 27721 / Reflection centric: 3884
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.5-501.71.10.56874
7.14-12.51.420.90.6420201
5-7.142.270.90.41088307
3.85-51.280.50.42070441
3.12-3.851.330.30.23355562
2.63-3.122.380.20.14946674
2.27-2.633.960.106829786
2-2.2710.960.108945839
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se38.65730.5010.0050.1920
2Se54.068360.0740.2470.2440
3Se41.734570.8690.5210.2050
4Se57.166450.1830.070.0870
5Se60.782470.2530.1950.0990
6Se54.617630.7160.6890.1780
7Se36.108890.8650.5180.1510
8Se66.165360.2020.6330.2520
9Se41.57910.530.9590.1550
10Se86.021610.6370.1580.1450
11Se52.607670.4080.0780.0240
12Se78.912870.8420.4490.0610
13Se77.323820.6670.8570.1230
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.5-500.2390.49901426874
7.14-12.50.3780.5580621420201
5-7.140.4280.549013951088307
3.85-50.4090.496025112070441
3.12-3.850.3940.46039173355562
2.63-3.120.3380.384056204946674
2.27-2.630.2130.237076156829786
2-2.270.1110.121097848945839
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 31605
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.23-10069.90.631512
6.49-8.2363.40.82514
5.57-6.4958.30.861571
4.95-5.5758.80.901629
4.5-4.9561.80.911703
4.16-4.557.50.91785
3.88-4.1655.80.902829
3.66-3.88580.912864
3.46-3.6657.30.889948
3.3-3.4658.50.908954
3.16-3.360.90.8741029
3.03-3.1658.80.8831031
2.92-3.0360.90.8711121
2.82-2.9261.20.861104
2.73-2.8263.80.861195
2.65-2.7363.60.8611192
2.57-2.6568.30.8451227
2.5-2.5770.30.8591284
2.44-2.567.70.8581285
2.38-2.4469.60.8521344
2.32-2.3870.40.861376
2.27-2.3272.10.8681379
2.22-2.2771.90.8481428
2.18-2.2271.70.8661454
2.13-2.18750.8491461
2.09-2.13770.8411526
2.06-2.0977.20.8281534
2-2.0682.90.7762326

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→33.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.423 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.165
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1595 5 %RANDOM
Rwork0.177 ---
all0.179 31604 --
obs0.179 31604 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.487 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2--0.21 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 2→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 18 342 3925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223659
X-RAY DIFFRACTIONr_bond_other_d0.0010.022502
X-RAY DIFFRACTIONr_angle_refined_deg1.4362.0014936
X-RAY DIFFRACTIONr_angle_other_deg0.92536187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8285454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27725.828151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76915709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3741510
X-RAY DIFFRACTIONr_chiral_restr0.0870.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023940
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02655
X-RAY DIFFRACTIONr_nbd_refined0.2180.2768
X-RAY DIFFRACTIONr_nbd_other0.1840.22529
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21794
X-RAY DIFFRACTIONr_nbtor_other0.0860.21817
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2253
X-RAY DIFFRACTIONr_metal_ion_refined0.0630.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.215
X-RAY DIFFRACTIONr_mcbond_it1.1831.52468
X-RAY DIFFRACTIONr_mcbond_other0.2431.5918
X-RAY DIFFRACTIONr_mcangle_it1.60323645
X-RAY DIFFRACTIONr_scbond_it2.68731525
X-RAY DIFFRACTIONr_scangle_it3.9594.51289
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 123 -
Rwork0.193 2031 -
all-2154 -
obs--93.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.997-0.32480.00931.91370.43231.07690.15220.08610.0144-0.1659-0.0707-0.1673-0.15460.0907-0.0815-0.0898-0.0250.0687-0.02560.0145-0.085614.42154.289814.5956
20.4406-0.09110.33020.8189-0.46351.31650.0233-0.02980.0391-0.02520.0284-0.0468-0.12850.0344-0.0517-0.09040.01470.032-0.0889-0.0171-0.064.901511.518638.6249
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 2318 - 234
2X-RAY DIFFRACTION2BB5 - 2318 - 234

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