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- PDB-3k1z: Crystal Structure of Human Haloacid Dehalogenase-like Hydrolase D... -

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Basic information

Entry
Database: PDB / ID: 3k1z
TitleCrystal Structure of Human Haloacid Dehalogenase-like Hydrolase Domain containing 3 (HDHD3)
ComponentsHaloacid dehalogenase-like hydrolase domain-containing protein 3
KeywordsHYDROLASE / HDHD3 / Haloacid Dehalogenase-like Hydrolase Domain containing 3 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


hydrolase activity / intracellular membrane-bounded organelle / nucleolus
Similarity search - Function
Haloacid dehalogenase-like hydrolase / HAD-superfamily hydrolase, subfamily IA, REG-2-like / 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 ...Haloacid dehalogenase-like hydrolase / HAD-superfamily hydrolase, subfamily IA, REG-2-like / 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
Haloacid dehalogenase-like hydrolase domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsUgochukwu, E. / Guo, K. / Yue, W.W. / Pilka, E. / Picaud, S. / Muniz, J. / Pike, A.C.W. / Krojer, T. / Gomes, M. / von Delft, F. ...Ugochukwu, E. / Guo, K. / Yue, W.W. / Pilka, E. / Picaud, S. / Muniz, J. / Pike, A.C.W. / Krojer, T. / Gomes, M. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Kavanagh, K. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Haloacid Dehalogenase-like Hydrolase Domain containing 3 (HDHD3)
Authors: Ugochukwu, E. / Guo, K. / Yue, W.W. / Pilka, E. / Kavanagh, K. / Oppermann, U.
History
DepositionSep 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloacid dehalogenase-like hydrolase domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0213
Polymers29,8671
Non-polymers1542
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.625, 62.455, 79.665
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Haloacid dehalogenase-like hydrolase domain-containing protein 3


Mass: 29867.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDHD3 / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q9BSH5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.49M NaH2PO4, 0.91M K2HPO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9773, 0.9796
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 7, 2009
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97731
20.97961
ReflectionResolution: 1.55→43.32 Å / Num. obs: 37908 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 11.5
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 2 / Num. unique all: 19357 / Rsym value: 0.552 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MAR345data collection
SHELXCDphasing
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.55→43.32 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.575 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.076 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20688 1892 5 %RANDOM
Rwork0.16744 ---
all0.16935 35966 --
obs0.16935 35966 99.27 %-
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 mean: 10.979 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.06 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.55→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 10 303 2208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211997
X-RAY DIFFRACTIONr_bond_other_d0.0010.021368
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9562727
X-RAY DIFFRACTIONr_angle_other_deg0.94333310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.74922.596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84215315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3371520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.87651225
X-RAY DIFFRACTIONr_mcbond_other1.1485491
X-RAY DIFFRACTIONr_mcangle_it3.87371969
X-RAY DIFFRACTIONr_scbond_it5.839772
X-RAY DIFFRACTIONr_scangle_it8.28411751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 130 -
Rwork0.297 2596 -
obs--97.78 %
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)
19.60896.34371.24644.76480.94880.57910.2628-0.72510.61620.1865-0.36680.4081-0.0107-0.2150.1040.1255-0.00290.02310.1465-0.03190.0745-19.2537-1.797610.8678
28.56910.2753-1.650.679-0.51212.48150.0358-0.4918-0.31760.0738-0.00740.06970.1715-0.1938-0.02840.0713-0.0322-0.01230.0720.0230.0383-17.2882-18.491512.0305
33.90963.05191.01693.81950.77191.338-0.0697-0.06790.4304-0.2025-0.07370.3919-0.1723-0.14120.14340.0660.0267-0.01240.0566-0.01450.0521-16.3299-0.04735.3911
43.4014-0.37860.86733.28320.40930.80520.00110.29660.1193-0.4542-0.07910.0741-0.13420.06180.0780.0857-0.0079-0.00850.0449-0.00060.0135-8.9571-0.87782.5155
53.90692.26660.40727.89981.48313.04580.00340.0898-0.1544-0.16050.0779-0.7517-0.10790.4822-0.08130.02730.00020.00540.1017-0.01430.09155.465-1.85069.5425
62.5345-0.42430.22682.94931.35783.9994-0.0365-0.24290.13490.14530.06650.0854-0.0816-0.0796-0.030.0323-0.00020.00470.0437-0.02410.0297-3.35017.299822.9046
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 31
2X-RAY DIFFRACTION2A32 - 81
3X-RAY DIFFRACTION3A82 - 129
4X-RAY DIFFRACTION4A130 - 157
5X-RAY DIFFRACTION5A158 - 182
6X-RAY DIFFRACTION6A183 - 247

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