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- PDB-5hl4: Acoustic injectors for drop-on-demand serial femtosecond crystall... -

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Basic information

Entry
Database: PDB / ID: 5hl4
TitleAcoustic injectors for drop-on-demand serial femtosecond crystallography
ComponentsRing-hydroxylating dioxygenase
KeywordsOXIDOREDUCTASE / RING-HYDROXYLATING DIOXYGENASE
Function / homology
Function and homology information


stachydrine N-demethylase / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich ...Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / COBALT HEXAMMINE(III) / Stachydrine N-demethylase
Similarity search - Component
Biological speciesSinorhizobium meliloti 1021 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRoessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F.R. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. ...Roessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F.R. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. / Cho, E. / Cohen, A.E. / Cowan, M. / Datwani, S. / Davidson, V.L. / Defever, J. / Eaton, B. / Ellson, R. / Feng, Y. / Ghislain, L.P. / Glownia, J.M. / Han, G. / Hattne, J. / Hellmich, J. / Heroux, A. / Ibrahim, M. / Kern, J. / Kuczewski, A. / Lemke, H.T. / Liu, P. / Majlof, L. / McClintock, W.M. / Myers, S. / Nelsen, S. / Olechno, J. / Orville, A.M. / Sauter, N.K. / Soares, A.S. / Soltis, M.S. / Song, H. / Stearns, R.G. / Tran, R. / Tsai, Y. / Uervirojnangkoorn, M. / Wilmot, C.M. / Yachandra, V. / Yano, J. / Yukl, E.T. / Zhu, D. / Zouni, A.
CitationJournal: Structure / Year: 2016
Title: Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography.
Authors: Roessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. / Cho, E. / Cohen, A.E. / Cowan, M. / ...Authors: Roessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. / Cho, E. / Cohen, A.E. / Cowan, M. / Datwani, S. / Davidson, V.L. / Defever, J. / Eaton, B. / Ellson, R. / Feng, Y. / Ghislain, L.P. / Glownia, J.M. / Han, G. / Hattne, J. / Hellmich, J. / Heroux, A. / Ibrahim, M. / Kern, J. / Kuczewski, A. / Lemke, H.T. / Liu, P. / Majlof, L. / McClintock, W.M. / Myers, S. / Nelsen, S. / Olechno, J. / Orville, A.M. / Sauter, N.K. / Soares, A.S. / Soltis, S.M. / Song, H. / Stearns, R.G. / Tran, R. / Tsai, Y. / Uervirojnangkoorn, M. / Wilmot, C.M. / Yachandra, V. / Yano, J. / Yukl, E.T. / Zhu, D. / Zouni, A.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Jan 24, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 14, 2018Group: Data collection / Source and taxonomy / Category: diffrn / entity_src_gen
Item: _diffrn.pdbx_serial_crystal_experiment / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.5Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Aug 26, 2026Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / pdbx_modification_feature ...chem_comp / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _chem_comp.formula / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ring-hydroxylating dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8184
Polymers46,4251
Non-polymers3933
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-28 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.427, 98.427, 180.087
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-503-

NCO

21A-503-

NCO

31A-503-

NCO

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Components

#1: Protein Ring-hydroxylating dioxygenase


Mass: 46425.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti 1021 (bacteria) / Strain: 1021 / Gene: SMa0751 / Production host: Sinorhizobium meliloti 1021 (bacteria) / References: UniProt: Q92ZP9
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10 mg/ml protein with 25 mM hexaamine cobalt chloride crystallized by hanging drop with precipitant 7.5% PEG 3350, 10% glycerol, and 0.1M HEPES pH 7.0.

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Data collection

DiffractionMean temperature: 295 K
Ambient temp details: Acoustic specimen injection into xfel beam
Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.36 Å
DetectorType: CS-PAD XPP / Detector: PIXEL / Date: Jun 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36 Å / Relative weight: 1
ReflectionResolution: 2.2→90.04 Å / Num. obs: 25584 / % possible obs: 99.66 % / Redundancy: 53.6 % / Net I/σ(I): 16.5
Reflection shellResolution: 2.2→2.29 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
cctbx.xfeldata reduction
cctbx.xfeldata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vcp

3vcp


Resolution: 2.2→90.04 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.756 / SU B: 11.033 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33012 1292 4.8 %RANDOM
Rwork0.26908 ---
obs0.27204 25584 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.081 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å2-0 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.2→90.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 12 134 3305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193258
X-RAY DIFFRACTIONr_bond_other_d0.0060.023026
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9494440
X-RAY DIFFRACTIONr_angle_other_deg0.88736951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0395395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3123.312154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.50215513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0331523
X-RAY DIFFRACTIONr_chiral_restr0.0930.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213678
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02781
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_it1.5762.5311586
X-RAY DIFFRACTIONr_mcbond_other1.5752.531585
X-RAY DIFFRACTIONr_mcangle_it2.563.7911979
X-RAY DIFFRACTIONr_mcangle_other2.5593.7931980
X-RAY DIFFRACTIONr_scbond_it1.2772.5371672
X-RAY DIFFRACTIONr_scbond_other1.2772.5371673
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0893.7632460
X-RAY DIFFRACTIONr_long_range_B_refined5.33319.653979
X-RAY DIFFRACTIONr_long_range_B_other5.33819.6713966
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.511 97 -
Rwork0.426 1803 -
obs--97.59 %

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