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- PDB-3l5k: The crystal structure of human Haloacid Dehalogenase-like Hydrola... -

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Basic information

Entry
Database: PDB / ID: 3l5k
TitleThe crystal structure of human Haloacid Dehalogenase-like Hydrolase Domain containing 1A (HDHD1A)
ComponentsHaloacid dehalogenase-like hydrolase domain-containing protein 1A
KeywordsHYDROLASE / HDHD1A / Haloacid Dehalogenase-like Hydrolase Domain containing 1A / Structural Genomics / Structural Genomics Consortium / SGC / Polymorphism
Function / homology
Function and homology information


pseudouridine 5'-phosphatase / pseudouridine 5'-phosphatase activity / pyrimidine nucleoside salvage / Pyrimidine salvage / nucleotide metabolic process / phosphatase activity / metal ion binding / cytosol
Similarity search - Function
Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / 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
: / Pseudouridine-5'-phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsUgochukwu, E. / Guo, K. / Picaud, S. / Muniz, J. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Ugochukwu, E. / Guo, K. / Picaud, S. / Muniz, J. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Yue, W.W. / Kavanagh, K.L. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human Haloacid Dehalogenase-like Hydrolase Domain containing 1A (HDHD1A)
Authors: Ugochukwu, E. / Guo, K. / Picaud, S. / Muniz, J. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Yue, W.W. / Kavanagh, K.L. / Oppermann, U. / ...Authors: Ugochukwu, E. / Guo, K. / Picaud, S. / Muniz, J. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Yue, W.W. / Kavanagh, K.L. / Oppermann, U. / Structural Genomics Consortium (SGC)
History
DepositionDec 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Haloacid dehalogenase-like hydrolase domain-containing protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2097
Polymers27,9361
Non-polymers2736
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.190, 85.190, 103.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Haloacid dehalogenase-like hydrolase domain-containing protein 1A / Protein GS1


Mass: 27936.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDHD1A / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q08623
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.86 Å3/Da / Density % sol: 68.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Sodium dihydrogen phosphate, 1.344 M di-potassium hydrogen phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→42.59 Å / Num. obs: 29508 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 9.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 2 / Num. unique all: 17548 / Rsym value: 0.855 / % possible all: 99

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PIB, 3HLT, 3K1Z, 2W4M

2pib
PDB Unreleased entry


Resolution: 2→42.6 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.824 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21272 1495 5.1 %RANDOM
Rwork0.16542 ---
all0.1677 28009 --
obs0.1677 28009 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.171 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20.4 Å20 Å2
2--0.81 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 11 217 2063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221887
X-RAY DIFFRACTIONr_bond_other_d0.0020.021296
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9882562
X-RAY DIFFRACTIONr_angle_other_deg0.96733195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2675240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76824.87278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04615332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.654157
X-RAY DIFFRACTIONr_chiral_restr0.0980.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212068
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_mcbond_it4.76351183
X-RAY DIFFRACTIONr_mcbond_other2.0135462
X-RAY DIFFRACTIONr_mcangle_it6.21271920
X-RAY DIFFRACTIONr_scbond_it10.2699704
X-RAY DIFFRACTIONr_scangle_it12.0411638
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 121 -
Rwork0.301 2009 -
obs--98.61 %
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)
12.0870.49070.21382.75670.30863.10850.04640.1048-0.0043-0.0723-0.0139-0.11030.0740.0742-0.03240.0080.0029-0.00190.05450.02030.0188-1.639437.89523.3434
23.03920.63540.59742.1069-0.71377.1363-0.09860.0303-0.05630.06170.0679-0.1634-0.39080.12320.03070.1607-0.0273-0.00580.03530.00110.09160.380961.99114.9082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 43
2X-RAY DIFFRACTION1A110 - 250
3X-RAY DIFFRACTION2A44 - 109

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