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- PDB-6q7o: Crystal structure of OE1 -

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Basic information

Entry
Database: PDB / ID: 6q7o
TitleCrystal structure of OE1
ComponentsOE1
KeywordsHYDROLASE / Computationally designed enzyme
Function / homology
Function and homology information


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
Glyceraldehyde 3-phosphate phosphatase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7302
Polymers27,6901
Non-polymers401
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-10 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.110, 70.530, 52.820
Angle α, β, γ (deg.)90.000, 104.240, 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

#1: Protein OE1


Mass: 27689.643 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
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris pH 8.5, 30 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2→41.43 Å / Num. obs: 16357 / % possible obs: 99.36 % / Redundancy: 3.3 % / Biso Wilson estimate: 36.05 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.039 / Rrim(I) all: 0.072 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.072 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 1603 / CC1/2: 0.94 / Rpim(I) all: 0.36 / % possible all: 99.38

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Processing

Software
NameVersionClassification
PHENIXdev_3304refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UW6
Resolution: 2→41.43 Å / SU ML: 0.2602 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.2594
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 822 5.03 %Random
Rwork0.192 ---
obs0.1939 16352 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.41 Å2
Refinement stepCycle: LAST / Resolution: 2→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 1 110 1958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232000
X-RAY DIFFRACTIONf_angle_d0.5062705
X-RAY DIFFRACTIONf_chiral_restr0.0373287
X-RAY DIFFRACTIONf_plane_restr0.0024354
X-RAY DIFFRACTIONf_dihedral_angle_d17.82311242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.130.29731400.27022567X-RAY DIFFRACTION99.19
2.13-2.290.30491330.24762572X-RAY DIFFRACTION99.05
2.29-2.520.27881410.23022585X-RAY DIFFRACTION99.45
2.52-2.880.28551250.23252580X-RAY DIFFRACTION99.63
2.88-3.630.24461420.1912585X-RAY DIFFRACTION99.49
3.63-51.210.17291410.15352641X-RAY DIFFRACTION99.39
Refinement TLS params.Method: refined / Origin x: 6.70627101222 Å / Origin y: 1.37985654173 Å / Origin z: 14.8362512245 Å
111213212223313233
T0.307903738304 Å2-0.0165271349498 Å2-0.000960134970305 Å2-0.311384565065 Å20.0588722718884 Å2--0.331052531329 Å2
L1.15781929175 °2-0.195413365708 °20.0143485688618 °2-1.02282604511 °20.28998830149 °2--0.848964977866 °2
S0.076838696124 Å °0.230623072647 Å °0.0538375693261 Å °0.0273427415616 Å °-0.0723808852794 Å °-0.00664093767737 Å °0.0150989579677 Å °-0.125391984961 Å °-1.60971445415E-5 Å °
Refinement TLS groupSelection details: all

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