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- PDB-3hlt: The crystal structure of human haloacid dehalogenase-like hydrola... -

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Basic information

Entry
Database: PDB / ID: 3hlt
TitleThe crystal structure of human haloacid dehalogenase-like hydrolase domain containing 2 (HDHD2)
ComponentsHDHD2
KeywordsHYDROLASE / HDHD2 / haloacid dehalogenase-like hydrolase domain containing 2 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


phosphatase activity / dephosphorylation / enzyme binding / extracellular exosome / metal ion binding
Similarity search - Function
HAD hydrolase, LHPP/HDHD2 / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Haloacid dehalogenase-like hydrolase domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsUgochukwu, E. / Shafqat, N. / Yue, W.W. / Cocking, R. / Bray, J.E. / Muniz, J.R.C. / Krojer, T. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Ugochukwu, E. / Shafqat, N. / Yue, W.W. / Cocking, R. / Bray, J.E. / Muniz, J.R.C. / Krojer, T. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human haloacid dehalogenase-like hydrolase domain containing 2 (HDHD2)
Authors: Ugochukwu, E. / Shafqat, N. / Yue, W.W. / Cocking, R. / Bray, J.E. / Muniz, J.R.C. / Krojer, T. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U. / ...Authors: Ugochukwu, E. / Shafqat, N. / Yue, W.W. / Cocking, R. / Bray, J.E. / Muniz, J.R.C. / Krojer, T. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / 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 / _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: HDHD2
C: HDHD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1918
Polymers58,8822
Non-polymers3096
Water1,15364
1
A: HDHD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5954
Polymers29,4411
Non-polymers1553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HDHD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5954
Polymers29,4411
Non-polymers1553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HDHD2
hetero molecules

C: HDHD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1918
Polymers58,8822
Non-polymers3096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2600 Å2
ΔGint-15 kcal/mol
Surface area21950 Å2
MethodPISA
4
A: HDHD2
hetero molecules

A: HDHD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1918
Polymers58,8822
Non-polymers3096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2660 Å2
ΔGint-12 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.940, 77.680, 103.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A7 - 70
2116C7 - 70
1216A179 - 260
2216C179 - 260
1124A71 - 178
2124C71 - 178

NCS ensembles :
ID
1
2

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Components

#1: Protein HDHD2 / / Haloacid dehalogenase-like hydrolase domain-containing protein 2


Mass: 29440.852 Da / Num. of mol.: 2 / Fragment: HDHD2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDHD2 / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: Q9H0R4
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.6 M Ammonium sulphate, 1% MPD, 0.1M HEPES 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: 0.9724 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.3→28.36 Å / Num. obs: 25410 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 10.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 1.5 / Num. unique all: 12741 / Rsym value: 0.804 / % possible all: 99.9

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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: 2HO4

2ho4


Resolution: 2.3→28.36 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 19.07 / SU ML: 0.21 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.32 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2658 1264 5 %RANDOM
Rwork0.21346 ---
all0.21598 21115 --
obs0.21598 24115 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.195 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---1.33 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 14 64 3708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223745
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9795105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48823.239142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01115565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6771527
X-RAY DIFFRACTIONr_chiral_restr0.0870.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212835
X-RAY DIFFRACTIONr_mcbond_it0.481.52499
X-RAY DIFFRACTIONr_mcangle_it0.87123969
X-RAY DIFFRACTIONr_scbond_it1.78431246
X-RAY DIFFRACTIONr_scangle_it2.7234.51131
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A868LOOSE POSITIONAL0.345
1C868LOOSE THERMAL2.1710
2A787MEDIUM POSITIONAL0.260.5
2C787MEDIUM THERMAL0.82
LS refinement shellResolution: 2.3→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 98 -
Rwork0.347 1740 -
obs--99.89 %
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)
19.07526.63841.81929.93860.35777.0184-0.1471-0.4938-0.0620.0704-0.3292-0.2184-0.05990.8110.47630.10080.0537-0.02980.510.14340.12329.8165-13.0707-15.6677
29.9749-1.0072-5.3273.6551-0.89284.8670.0092-0.1076-0.0915-0.4245-0.0314-0.02240.10760.42190.02220.17410.02570.01940.37880.06370.039824.7791-8.589-20.1187
38.7104-1.5554-0.70560.6282-0.23691.35680.06540.51270.1596-0.1597-0.0430.0312-0.0033-0.0988-0.02240.1544-0.01820.01190.29290.09340.080610.5529-3.6736-20.1507
47.29420.0621-1.36742.68080.47956.15780.04670.0510.2341-0.1365-0.0076-0.05560.14140.1263-0.03920.0412-0.02390.00480.10340.04080.02972.3557-6.7046-5.8477
58.34461.5959-1.60496.8614-2.07964.5945-0.2084-0.4435-0.915-0.1155-0.274-0.20470.92880.47490.48240.34310.12130.08260.33930.07240.246723.8222-22.49-14.026
68.84713.7449-2.253410.1969-2.98585.40660.2270.8476-0.977-2.1921-0.4879-0.74591.72270.57060.2611.41410.4926-0.11780.51-0.10950.768427.548424.0335-15.3292
78.12040.6368-4.40435.3876-0.61884.02420.2844-1.0425-0.9326-1.1262-0.3848-0.28290.5590.9170.10040.84020.2852-0.42860.4467-0.0130.826921.713316.662-0.8794
88.4376-0.2015-5.10362.1533-0.03973.8404-0.0792-0.29140.14270.20210.1172-0.26040.36020.2017-0.0380.69130.0468-0.48190.1192-0.06160.55576.382920.12950.3445
98.1238-4.40841.333410.8088-6.20429.01220.39940.20680.52-1.0263-0.31590.44260.4990.0982-0.08350.56720.06-0.11310.2022-0.04930.581423.701634.8859-10.0959
102.6227-1.6354-2.371211.35313.984712.38990.27371.12770.009-1.6503-0.43940.11370.58850.02310.16580.9750.2539-0.07410.65610.06910.707322.679338.2535-22.6753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 31
2X-RAY DIFFRACTION2A32 - 59
3X-RAY DIFFRACTION3A60 - 117
4X-RAY DIFFRACTION4A118 - 179
5X-RAY DIFFRACTION5A180 - 260
6X-RAY DIFFRACTION6C6 - 59
7X-RAY DIFFRACTION7C60 - 119
8X-RAY DIFFRACTION8C120 - 180
9X-RAY DIFFRACTION9C181 - 224
10X-RAY DIFFRACTION10C225 - 259

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