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- PDB-4kaa: Crystal structure of the halotag2 protein at the resolution 2.3A,... -

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Basic information

Entry
Database: PDB / ID: 4kaa
TitleCrystal structure of the halotag2 protein at the resolution 2.3A, Northeast Structural Genomics Consortium (NESG) target OR150
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.276 Å
AuthorsKuzin, A. / Lew, S. / Neklesa, T.K. / Noblin, D. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, H. / Everett, J.K. ...Kuzin, A. / Lew, S. / Neklesa, T.K. / Noblin, D. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Crews, C. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target OR150
Authors: Kuzin, A. / Lew, S. / Neklesa, T.K. / Noblin, D. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Crews, C. / Tong, L.
History
DepositionApr 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Haloalkane dehalogenase
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1235
Polymers69,9712
Non-polymers1523
Water5,765320
1
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0092
Polymers34,9861
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1153
Polymers34,9861
Non-polymers1292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.630, 91.262, 98.157
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 Haloalkane dehalogenase /


Mass: 34985.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Gene: dhaA / References: UniProt: P0A3G3, haloalkane dehalogenase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277 K / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:CaCl2 0.1M, MES 0.1M, PEG 8000 40%, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 18, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.276→30 Å / Num. obs: 52782 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 21.15 Å2 / Rmerge(I) obs: 0.085

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1269refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BN7

1bn7


Resolution: 2.276→29.613 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.24 / σ(F): 1.33 / Phase error: 23.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 1392 5.02 %
Rwork0.1668 --
obs0.1701 27706 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.828 Å2
Refinement stepCycle: LAST / Resolution: 2.276→29.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4680 0 9 320 5009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084901
X-RAY DIFFRACTIONf_angle_d1.1696709
X-RAY DIFFRACTIONf_dihedral_angle_d13.841806
X-RAY DIFFRACTIONf_chiral_restr0.085707
X-RAY DIFFRACTIONf_plane_restr0.006888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2764-2.35780.31721240.19462474X-RAY DIFFRACTION90
2.3578-2.45210.27571390.17832736X-RAY DIFFRACTION100
2.4521-2.56370.25641440.16722746X-RAY DIFFRACTION100
2.5637-2.69880.24911270.17082765X-RAY DIFFRACTION100
2.6988-2.86770.25271640.17252736X-RAY DIFFRACTION100
2.8677-3.08890.25751640.17862739X-RAY DIFFRACTION100
3.0889-3.39940.22191580.1822762X-RAY DIFFRACTION100
3.3994-3.89030.25321010.18661842X-RAY DIFFRACTION71
3.8903-4.89780.2071230.13532566X-RAY DIFFRACTION99
4.8978-29.61510.1681480.15082948X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.0994 Å / Origin y: -3.6985 Å / Origin z: 36.4341 Å
111213212223313233
T0.1378 Å20.001 Å2-0.0155 Å2-0.1439 Å20.0108 Å2--0.1787 Å2
L0.6651 °2-0.1171 °2-0.6979 °2-0.0928 °20.1077 °2--1.2481 °2
S0.02 Å °0.0153 Å °0.0217 Å °0.0079 Å °-0.0177 Å °-0.0057 Å °-0.0468 Å °-0.0001 Å °-0.0004 Å °
Refinement TLS groupSelection details: all

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