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- PDB-5hif: Crystal structure of a reconstructed lactonase ancestor, Anc1-MPH... -

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Basic information

Entry
Database: PDB / ID: 5hif
TitleCrystal structure of a reconstructed lactonase ancestor, Anc1-MPH, of the bacterial methyl parathion hydrolase, MPH.
Componentsreconstructed lactonase ancestor, Anc1-MPH
KeywordsHYDROLASE / ancestral reconstruction / lactonase / methyl parathion hydrolase
Function / homologyRibonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / 4-Layer Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBaier, F. / Carr, P.D. / Jackson, C.J.
CitationJournal: To Be Published
Title: to be published
Authors: Baier, F. / Carr, P.D. / Jackson, C.J.
History
DepositionJan 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: reconstructed lactonase ancestor, Anc1-MPH
B: reconstructed lactonase ancestor, Anc1-MPH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5349
Polymers63,0352
Non-polymers4987
Water8,647480
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-174 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.600, 88.150, 119.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: -4 - 294 / Label seq-ID: 1 - 299

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein reconstructed lactonase ancestor, Anc1-MPH


Mass: 31517.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b
Details (production host): N-terminal MBP-tag with TEV cleavage site
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (D3) / References: EC: 3.1.1.35
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium acetate terahydrate 20% PEG 3350 10mM Tris/HCl 50mM NaCl 0.1mM ZnCl2
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: oxford cryostream
Diffraction sourceSource: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2015 / Details: MARMUX
RadiationMonochromator: micro source / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→33.6 Å / Num. obs: 78672 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 11.078 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4.9 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1p9e.ent

1p9e


Resolution: 1.6→33.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.544 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 3965 5 %RANDOM
Rwork0.1739 ---
obs0.17553 74621 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.322 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4444 0 19 480 4943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194648
X-RAY DIFFRACTIONr_bond_other_d0.0080.024460
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.9616323
X-RAY DIFFRACTIONr_angle_other_deg1.302310311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46825.238189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96715733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9091511
X-RAY DIFFRACTIONr_chiral_restr0.1250.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215368
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021019
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_it1.7541.612421
X-RAY DIFFRACTIONr_mcbond_other1.7551.6092420
X-RAY DIFFRACTIONr_mcangle_it2.442.4123031
X-RAY DIFFRACTIONr_mcangle_other2.442.4133032
X-RAY DIFFRACTIONr_scbond_it2.6881.8772227
X-RAY DIFFRACTIONr_scbond_other2.6871.8772227
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9652.6763280
X-RAY DIFFRACTIONr_long_range_B_refined5.25513.8545506
X-RAY DIFFRACTIONr_long_range_B_other5.1913.4215254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17029 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.597→1.638 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 266 -
Rwork0.216 5059 -
obs--89.71 %

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