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- PDB-3t1g: Engineering of organophosphate hydrolase by computational design ... -

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Basic information

Entry
Database: PDB / ID: 3t1g
TitleEngineering of organophosphate hydrolase by computational design and directed evolution
Componentsorganophosphate hydrolase
KeywordsHYDROLASE / Computational design / directed evolution / TIM beta/alpha-barrel / Metallo-dependent hydrolase / Organophosphate binding / Hydrolysis / Artificial enzyme
Function / homology
Function and homology information


mature B cell apoptotic process / purine nucleotide salvage / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of mucus secretion / penile erection / purine nucleoside binding ...mature B cell apoptotic process / purine nucleotide salvage / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of mucus secretion / penile erection / purine nucleoside binding / positive regulation of germinal center formation / negative regulation of adenosine receptor signaling pathway / inosine biosynthetic process / histamine secretion / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / amide catabolic process / adenosine deaminase / hypoxanthine biosynthetic process / germinal center B cell differentiation / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / inhibition of non-skeletal tissue mineralization / deaminase activity / deoxyadenosine catabolic process / dAMP catabolic process / AMP catabolic process / adenosine metabolic process / positive regulation of T cell differentiation in thymus / dATP catabolic process / negative regulation of leukocyte migration / mucus secretion / GMP salvage / response to purine-containing compound / regulation of cell-cell adhesion mediated by integrin / embryonic digestive tract development / allantoin metabolic process / trophectodermal cell differentiation / IMP salvage / positive regulation of smooth muscle contraction / germinal center formation / Peyer's patch development / negative regulation of mature B cell apoptotic process / AMP salvage / regulation of T cell differentiation in thymus / anchoring junction / negative regulation of thymocyte apoptotic process / positive regulation of alpha-beta T cell differentiation / alpha-beta T cell differentiation / positive regulation of T cell differentiation / regulation of T cell differentiation / positive regulation of heart rate / lung alveolus development / positive regulation of T cell receptor signaling pathway / leukocyte migration / thymocyte apoptotic process / B cell proliferation / T cell differentiation / smooth muscle contraction / response to inorganic substance / response to vitamin E / positive regulation of calcium-mediated signaling / positive regulation of B cell proliferation / dendrite cytoplasm / T cell activation / liver development / placenta development / calcium-mediated signaling / lung development / negative regulation of inflammatory response / positive regulation of T cell activation / T cell differentiation in thymus / T cell receptor signaling pathway / in utero embryonic development / lysosome / response to hypoxia / cell adhesion / external side of plasma membrane / neuronal cell body / apoptotic process / negative regulation of apoptotic process / cell surface / extracellular space / zinc ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Adenosine deaminase / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsTakeuchi, R. / Stoddard, B.L.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.
Authors: Khare, S.D. / Kipnis, Y. / Greisen, P.J. / Takeuchi, R. / Ashani, Y. / Goldsmith, M. / Song, Y. / Gallaher, J.L. / Silman, I. / Leader, H. / Sussman, J.L. / Stoddard, B.L. / Tawfik, D.S. / Baker, D.
History
DepositionJul 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_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: organophosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4826
Polymers40,1811
Non-polymers3025
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.391, 77.592, 94.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein organophosphate hydrolase


Mass: 40180.672 Da / Num. of mol.: 1 / Mutation: D19S,L58Q,F61T,F65W,Q138H,A183I,V218F,D296A,I299E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adenosine deaminase, ADA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P03958, Hydrolases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Tris-HCl, 0.2 M calcium acetate, 20% PEG3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 2, 2010
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 15204 / Num. obs: 14900 / % possible obs: 98 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 31.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 5.4 / Num. unique all: 1332 / % possible all: 91.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FKW

1fkw


Resolution: 2.35→42.4 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / SU B: 16.989 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.508 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24993 755 5.1 %RANDOM
Rwork0.18949 ---
obs0.1925 14116 98 %-
all-14404 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.089 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.35→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 5 136 2937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222862
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.9633875
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13924.519135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13715508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4361515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212173
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3581.51741
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70322819
X-RAY DIFFRACTIONr_scbond_it1.17531121
X-RAY DIFFRACTIONr_scangle_it1.9784.51056
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 44 -
Rwork0.219 946 -
obs--91.67 %
Refinement TLS params.Method: refined / Origin x: 13.831 Å / Origin y: -11.12 Å / Origin z: -16.069 Å
111213212223313233
T0.037 Å2-0.0195 Å20.012 Å2-0.0487 Å2-0.0273 Å2--0.0173 Å2
L1.4608 °2-0.1356 °2-0.5712 °2-1.6699 °20.2734 °2--1.9001 °2
S-0.0617 Å °0.0429 Å °-0.036 Å °-0.0436 Å °-0.0014 Å °0.0197 Å °0.0213 Å °-0.0057 Å °0.0631 Å °

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