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- PDB-4nao: Crystal structure of EasH -

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Basic information

Entry
Database: PDB / ID: 4nao
TitleCrystal structure of EasH
ComponentsPutative oxygenase
KeywordsOXIDOREDUCTASE / jelly-roll fold / Fe binding
Function / homology
Function and homology information


indole alkaloid biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / dioxygenase activity / metal ion binding
Similarity search - Function
q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Dioxygenase easH
Similarity search - Component
Biological speciesClaviceps purpurea (ergot fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.649 Å
AuthorsJanke, R. / Havemann, J. / Vogel, D. / Keller, U. / Loll, B.
CitationJournal: Chem.Biol. / Year: 2014
Title: Cyclolization of d-lysergic Acid alkaloid peptides.
Authors: Havemann, J. / Vogel, D. / Loll, B. / Keller, U.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Putative oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3965
Polymers36,8891
Non-polymers5074
Water3,405189
1
A: Putative oxygenase
hetero molecules

A: Putative oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,79210
Polymers73,7772
Non-polymers1,0158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6970 Å2
ΔGint-77 kcal/mol
Surface area23600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.304, 91.304, 79.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-525-

HOH

31A-640-

HOH

41A-651-

HOH

51A-653-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -y+1,-x+1,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative oxygenase /


Mass: 36888.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Claviceps purpurea (ergot fungus) / Strain: D11 / Gene: easH1 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: G8GV69

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Non-polymers , 5 types, 193 molecules

#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 40% (v/v) PEG 600, 125 mM Na3citrate at pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.24908 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 22, 2013
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24908 Å / Relative weight: 1
ReflectionResolution: 1.62→40 Å / Num. all: 80988 / Num. obs: 80988 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 8.4 % / Biso Wilson estimate: 20.32 Å2
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 5.1 % / % possible all: 96.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.649→36.326 Å / SU ML: 0.14 / σ(F): 1.51 / Phase error: 16.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1819 3859 5.01 %RANDOM
Rwork0.1571 ---
obs0.1583 76981 99.81 %-
all-76981 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.649→36.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 22 189 2451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132406
X-RAY DIFFRACTIONf_angle_d1.4693268
X-RAY DIFFRACTIONf_dihedral_angle_d14.989956
X-RAY DIFFRACTIONf_chiral_restr0.107355
X-RAY DIFFRACTIONf_plane_restr0.007432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6488-1.66890.21731310.22142506X-RAY DIFFRACTION97
1.6689-1.690.25181370.20392620X-RAY DIFFRACTION99
1.69-1.71220.24231420.18732604X-RAY DIFFRACTION100
1.7122-1.73570.23481320.18782600X-RAY DIFFRACTION100
1.7357-1.76050.19041350.18042650X-RAY DIFFRACTION100
1.7605-1.78670.18861350.17082574X-RAY DIFFRACTION100
1.7867-1.81470.2061360.17732609X-RAY DIFFRACTION100
1.8147-1.84440.17481400.172640X-RAY DIFFRACTION100
1.8444-1.87620.18811370.16822599X-RAY DIFFRACTION100
1.8762-1.91030.20671400.16142620X-RAY DIFFRACTION100
1.9103-1.94710.22171360.15262630X-RAY DIFFRACTION100
1.9471-1.98680.16741390.14682638X-RAY DIFFRACTION100
1.9868-2.030.14481370.14192600X-RAY DIFFRACTION100
2.03-2.07720.18221360.14442637X-RAY DIFFRACTION100
2.0772-2.12920.21381380.14812598X-RAY DIFFRACTION100
2.1292-2.18670.16881400.1472615X-RAY DIFFRACTION100
2.1867-2.25110.16861390.14692605X-RAY DIFFRACTION100
2.2511-2.32370.18551450.14812627X-RAY DIFFRACTION100
2.3237-2.40680.19181360.15382627X-RAY DIFFRACTION100
2.4068-2.50310.19771340.15272589X-RAY DIFFRACTION100
2.5031-2.6170.14681410.15672626X-RAY DIFFRACTION100
2.617-2.75490.18811400.15332608X-RAY DIFFRACTION100
2.7549-2.92740.19291410.1592624X-RAY DIFFRACTION100
2.9274-3.15340.18791370.1642621X-RAY DIFFRACTION100
3.1534-3.47050.16321410.15492596X-RAY DIFFRACTION100
3.4705-3.97210.15921430.14292635X-RAY DIFFRACTION100
3.9721-5.00240.17391400.13342600X-RAY DIFFRACTION100
5.0024-36.33470.19341310.19322624X-RAY DIFFRACTION100
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)
12.05990.3204-0.04633.7341.00973.57690.0243-0.00130.01270.1567-0.0038-0.5751-0.12770.6826-0.10170.0986-0.0325-0.01670.2194-0.02790.180887.041433.469736.2698
21.26570.08850.22061.5130.31522.054-0.0107-0.14120.04310.2014-0.05650.16620.1245-0.19420.03460.1235-0.03390.02190.108-0.01330.133467.448432.346837.228
30.92410.1460.14361.72230.71161.70710.0275-0.1164-0.04010.20340.013-0.0670.16350.1219-0.03430.105-0.01560.02040.10830.00560.130773.147628.424335.4863
42.1553-0.2969-0.01755.82872.70263.6794-0.2029-0.06140.37930.01280.01460.3261-0.57580.02840.15090.28650.0022-0.03480.15250.04460.257863.439943.747516.7815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 10:36)
2X-RAY DIFFRACTION2(chain A and resid 37:146)
3X-RAY DIFFRACTION3(chain A and resid 147:273)
4X-RAY DIFFRACTION4(chain A and resid 274:309)

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