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- PDB-6q7p: Crystal structure of OE1.2 -

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Basic information

Entry
Database: PDB / ID: 6q7p
TitleCrystal structure of OE1.2
ComponentsOE1.2
KeywordsHYDROLASE / Computationally designed enzyme
Function / homology
Function and homology information


small molecule biosynthetic process / cellular biosynthetic process / organonitrogen compound biosynthetic process / phosphatase activity
Similarity search - Function
HAD-superfamily hydrolase, subfamily IA, CTE7 / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...HAD-superfamily hydrolase, subfamily IA, CTE7 / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / 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
1-PHENYLETHANONE / TRIETHYLENE GLYCOL / Glyceraldehyde 3-phosphate phosphatase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M027023/1 United Kingdom
European Research Council757991 United Kingdom
CitationJournal: Nature / Year: 2019
Title: Design and evolution of an enzyme with a non-canonical organocatalytic mechanism.
Authors: Burke, A.J. / Lovelock, S.L. / Frese, A. / Crawshaw, R. / Ortmayer, M. / Dunstan, M. / Levy, C. / Green, A.P.
History
DepositionDec 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OE1.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0906
Polymers27,6381
Non-polymers4535
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-11 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.980, 71.310, 52.890
Angle α, β, γ (deg.)90.000, 105.280, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein OE1.2


Mass: 27637.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0459 / Production host: Escherichia coli (E. coli) / References: UniProt: O58216

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Non-polymers , 6 types, 121 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-AC0 / 1-PHENYLETHANONE / ACETOPHENONE / Acetophenone


Mass: 120.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 47.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.05 M magnesium sulfate heptahydrate, 0.1 M HEPES pH 7.5, 28 % v/v PEG Smear Medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.96→41.49 Å / Num. obs: 17448 / % possible obs: 99.46 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Net I/σ(I): 11.15
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 1718 / CC1/2: 0.83 / Rpim(I) all: 0.3 / % possible all: 98.85

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Processing

Software
NameVersionClassification
PHENIXdev_3304refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UW6

2uw6


Resolution: 1.96→41.49 Å / SU ML: 0.2049 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.0526
RfactorNum. reflection% reflection
Rfree0.2134 906 5.19 %
Rwork0.172 --
obs0.1739 17442 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.04 Å2
Refinement stepCycle: LAST / Resolution: 1.96→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 29 116 1990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051924
X-RAY DIFFRACTIONf_angle_d0.7432582
X-RAY DIFFRACTIONf_chiral_restr0.0446274
X-RAY DIFFRACTIONf_plane_restr0.004331
X-RAY DIFFRACTIONf_dihedral_angle_d15.63971157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.080.26581670.2342687X-RAY DIFFRACTION99.03
2.08-2.240.25811460.20632773X-RAY DIFFRACTION99.35
2.24-2.470.20911690.18212714X-RAY DIFFRACTION99.48
2.47-2.830.20751490.18252767X-RAY DIFFRACTION99.52
2.83-3.560.21661580.18252753X-RAY DIFFRACTION99.76
3.56-41.50.19671170.14862842X-RAY DIFFRACTION99.63
Refinement TLS params.Method: refined / Origin x: 6.4315761747 Å / Origin y: 0.855885274453 Å / Origin z: 14.924004571 Å
111213212223313233
T0.224919953326 Å2-0.00971650551877 Å20.00845190493569 Å2-0.232801418125 Å20.06876069197 Å2--0.250957739627 Å2
L1.2681870409 °2-0.120172660022 °2-0.294474187416 °2-1.45251983451 °20.655308999002 °2--1.79668020139 °2
S0.047866941363 Å °0.182873660954 Å °0.0881044625499 Å °0.0457622008333 Å °-0.0536441973228 Å °0.00291150651452 Å °0.0124916895952 Å °-0.125590952438 Å °0.00566526710445 Å °
Refinement TLS groupSelection details: all

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