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- PDB-4kyv: Crystal Structure of dehalogenase HaloTag2 with HALTS at the reso... -

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Basic information

Entry
Database: PDB / ID: 4kyv
TitleCrystal Structure of dehalogenase HaloTag2 with HALTS at the resolution 1.8A. Northeast Structural Genomics Consortium (NESG) Target OR150
Componentsdehalogenase HaloTag2
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / HALTS / halogenase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-1Q9
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å
AuthorsKuzin, A. / Lew, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, H. / Everett, J.K. / Acton, T.B. / Kornhaber, G. ...Kuzin, A. / Lew, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, H. / Everett, J.K. / Acton, T.B. / Kornhaber, G. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target OR150
Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, H. / Everett, J.K. / Acton, T.B. / Kornhaber, G. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 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: dehalogenase HaloTag2
B: dehalogenase HaloTag2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4908
Polymers69,9032
Non-polymers5876
Water12,250680
1
A: dehalogenase HaloTag2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2454
Polymers34,9521
Non-polymers2933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: dehalogenase HaloTag2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2454
Polymers34,9521
Non-polymers2933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.938, 94.770, 73.483
Angle α, β, γ (deg.)90.000, 93.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein dehalogenase HaloTag2


Mass: 34951.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET15_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic
#2: Chemical ChemComp-1Q9 / N-(2-ethoxy-3,5-dimethylbenzyl)-1H-tetrazol-5-amine


Mass: 247.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N5O
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 42.41 %
Crystal growMethod: microbatch under oil / pH: 5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:.1M NH4NO3 .1M Sodium Acetate 24% PEG 20000 , microbatch under oil

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 56625 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 13.43 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 26.8

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1269refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KAC

4kac


Resolution: 1.796→29.61 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.907 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 17.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3853 3.79 %random
Rwork0.153 ---
obs0.154 101600 94.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.38 Å2 / Biso mean: 18.57 Å2 / Biso min: 7.97 Å2
Refinement stepCycle: LAST / Resolution: 1.796→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4785 0 40 680 5505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075010
X-RAY DIFFRACTIONf_angle_d1.1226853
X-RAY DIFFRACTIONf_chiral_restr0.077715
X-RAY DIFFRACTIONf_plane_restr0.007901
X-RAY DIFFRACTIONf_dihedral_angle_d12.7731825
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.796-1.8180.2611490.2123250339988
1.818-1.8410.2471270.2053325345291
1.841-1.8650.2461210.1973428354991
1.865-1.8910.2571410.193375351692
1.891-1.9180.2371380.1883333347192
1.918-1.9470.2261320.183449358191
1.947-1.9770.2411200.1793407352792
1.977-2.010.2241540.1693390354493
2.01-2.0440.2061160.1723509362592
2.044-2.0810.2241470.1643363351093
2.081-2.1210.2211190.1623466358593
2.121-2.1650.2121440.1593488363293
2.165-2.2120.1921480.1543445359394
2.212-2.2630.181320.1543512364494
2.263-2.320.1931310.1453483361495
2.32-2.3820.1761480.1463585373395
2.382-2.4520.1641430.1453469361296
2.452-2.5320.1931370.1493621375896
2.532-2.6220.1941440.1493574371897
2.622-2.7270.21400.1493619375997
2.727-2.8510.1731390.1483597373697
2.851-3.0010.2111430.1543584372798
3.001-3.1890.1781510.1513602375397
3.189-3.4350.1851310.1453584371597
3.435-3.780.1381360.1423649378598
3.78-4.3250.141390.1273629376897
4.325-5.4440.1611470.1253534368196
5.444-29.6140.1741360.1583477361394
Refinement TLS params.Method: refined / Origin x: 10.4718 Å / Origin y: 10.2827 Å / Origin z: 20.2585 Å
111213212223313233
T0.0832 Å2-0.0007 Å2-0.0134 Å2-0.0984 Å20.0082 Å2--0.1173 Å2
L0.1144 °2-0.1004 °2-0.1862 °2-0.3206 °20.2758 °2--0.5163 °2
S-0.0066 Å °0.009 Å °0.0057 Å °-0.0075 Å °-0.0203 Å °0.0221 Å °-0.0009 Å °-0.0161 Å °0.0304 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 306
2X-RAY DIFFRACTION1allB4 - 306
3X-RAY DIFFRACTION1allA - B1 - 401
4X-RAY DIFFRACTION1allA - B1 - 799
5X-RAY DIFFRACTION1allA - B1 - 403

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