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- PDB-4rzm: Crystal structure of the Lsd19-lasalocid A complex -

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Basic information

Entry
Database: PDB / ID: 4rzm
TitleCrystal structure of the Lsd19-lasalocid A complex
ComponentsEpoxide hydrolase LasB
KeywordsISOMERASE / NTF2-like fold / epoxide-opening cyclic ether formation / isomerization
Function / homology
Function and homology information


Isomerases; Intramolecular lyases / antibiotic biosynthetic process / isomerase activity
Similarity search - Function
SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Lasalocid A / Epoxide hydrolase LasB
Similarity search - Component
Biological speciesStreptomyces lasaliensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsMathews, I.I. / Hotta, K. / Chen, X. / Kim, C.-Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Epoxide hydrolase-lasalocid a structure provides mechanistic insight into polyether natural product biosynthesis.
Authors: Wong, F.T. / Hotta, K. / Chen, X. / Fang, M. / Watanabe, K. / Kim, C.Y.
History
DepositionDec 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
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_ncs_dom_lim / 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_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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _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: Epoxide hydrolase LasB
B: Epoxide hydrolase LasB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,92018
Polymers61,0822
Non-polymers1,83816
Water2,684149
1
A: Epoxide hydrolase LasB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3857
Polymers30,5411
Non-polymers8446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epoxide hydrolase LasB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,53511
Polymers30,5411
Non-polymers99410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Epoxide hydrolase LasB
B: Epoxide hydrolase LasB
hetero molecules

A: Epoxide hydrolase LasB
B: Epoxide hydrolase LasB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,84036
Polymers122,1634
Non-polymers3,67732
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area11380 Å2
ΔGint-99 kcal/mol
Surface area43450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.140, 140.140, 198.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-310-

CL

21A-445-

HOH

31A-477-

HOH

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: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: -2 - 280 / Label seq-ID: 1 - 283

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Epoxide hydrolase LasB / Lasalocid biosynthesis protein Lsd19


Mass: 30540.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lasaliensis (bacteria) / Gene: lasB, lsd19 / Plasmid: pCold1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B6ZK72, Isomerases; Intramolecular lyases

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Non-polymers , 6 types, 165 molecules

#2: Chemical ChemComp-LSD / Lasalocid A / 6-[(3R,4S,5S,7R)-7-{(2S,3S,5S)-5-ethyl-5-[(2R,5R,6S)-5-ethyl-5-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]-3-methyltetrahydrofuran-2-yl}-4-hydroxy-3,5-dimethyl-6-oxononyl]-2-hydroxy-3-methylbenzoic acid


Mass: 590.788 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H54O8 / Comment: antibiotic*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.99 Å3/Da / Density % sol: 69.16 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.65 M sodium formate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.33→38.16 Å / Num. all: 42332 / Num. obs: 42332 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.95
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 2.45 / Num. unique all: 3074 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RGA

3rga


Resolution: 2.33→38.16 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 10.395 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20671 2137 5 %RANDOM
Rwork0.17734 ---
obs0.17887 40197 99.79 %-
all-42337 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.566 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å20 Å2
2--1.74 Å20 Å2
3----3.48 Å2
Refinement stepCycle: LAST / Resolution: 2.33→38.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4216 0 124 149 4489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194422
X-RAY DIFFRACTIONr_bond_other_d0.0040.023023
X-RAY DIFFRACTIONr_angle_refined_deg1.83826018
X-RAY DIFFRACTIONr_angle_other_deg1.18437304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1255556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.25121.72186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44615677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5191556
X-RAY DIFFRACTIONr_chiral_restr0.1020.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214928
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02904
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9691 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 157 -
Rwork0.257 2695 -
obs--99.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.82890.2938-1.81691.3257-0.7473.2290.1190.11690.0975-0.079-0.0203-0.1282-0.13030.1119-0.09880.0276-0.02190.00030.0580.03120.053121.919320.992943.0919
22.45040.1429-0.71931.2385-0.08382.8172-0.07480.33050.05810.00050.02940.2078-0.0421-0.39320.04540.0245-0.0295-0.03520.11280.04370.08850.672717.480144.7871
31.04410.48350.11222.8262-0.9561.54970.0458-0.10840.12850.3610.04950.1743-0.2248-0.122-0.09520.08670.00750.06080.0313-0.01770.0649-19.189-8.495977.3574
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 87
2X-RAY DIFFRACTION2A97 - 280
3X-RAY DIFFRACTION3B-2 - 280

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