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- PDB-4xcb: Crystal Structure of HygX from Streptomyces hygroscopicus with ni... -

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Basic information

Entry
Database: PDB / ID: 4xcb
TitleCrystal Structure of HygX from Streptomyces hygroscopicus with nickel, 2-oxoglutarate, and hygromycin B bound
Componentsoxidase/hydroxylase
KeywordsOXIDOREDUCTASE / double stranded beta helix
Function / homology
Function and homology information


2-oxoglutarate-dependent dioxygenase activity / metal ion binding
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / HYGROMYCIN B VARIANT / NICKEL (II) ION / Putative oxidase/hydroxylase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus subsp. hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMcCulloch, K.M. / McCranie, E.K. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily.
Authors: McCulloch, K.M. / McCranie, E.K. / Smith, J.A. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.journal_id_CSD ..._chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _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.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.value / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: oxidase/hydroxylase
B: oxidase/hydroxylase
C: oxidase/hydroxylase
D: oxidase/hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,38516
Polymers117,4564
Non-polymers2,92912
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15760 Å2
ΔGint-120 kcal/mol
Surface area36470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.220, 117.431, 185.359
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein
oxidase/hydroxylase


Mass: 29363.971 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus subsp. hygroscopicus (bacteria)
Gene: hygX / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2MFS1
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-HY0 / HYGROMYCIN B VARIANT / (2R,3'R,3aS,4S,4'S,5'R,6R,6'R,7S,7aS)-4-[(1R,2S,3R,5S,6R)-3-azanyl-2,6-dihydroxy-5-(methylamino)cyclohexyl]oxy-6'-[(1S) -1-azanyl-2-hydroxy-ethyl]-6-(hydroxymethyl)spiro[4,6,7,7a-tetrahydro-3aH-[1,3]dioxolo[4,5-c]pyran-2,2'-oxane]-3',4',5', 7-tetrol


Mass: 527.520 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H37N3O13
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 100 mM MES, 18% PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 126988 / % possible obs: 86.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 15.42 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.03 / Rrim(I) all: 0.062 / Χ2: 1.302 / Net I/av σ(I): 25.668 / Net I/σ(I): 10.7 / Num. measured all: 461160
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.633.20.34460190.8930.2120.4070.57782.7
1.63-1.663.20.29160100.9360.1770.3430.60483.3
1.66-1.693.30.25960720.9440.1570.3050.6182.9
1.69-1.723.30.21960970.9590.130.2560.63984.1
1.72-1.763.30.18161240.9710.1070.2120.65284.2
1.76-1.83.40.16861770.9740.0980.1960.6984.5
1.8-1.853.50.13860780.9850.0790.160.71884.1
1.85-1.93.60.12561340.9860.0710.1440.79684.1
1.9-1.953.70.10861170.990.060.1240.89783.7
1.95-2.023.80.09360670.9920.050.1060.94782.5
2.02-2.093.80.08259980.9940.0440.0931.06782.4
2.09-2.173.90.07559560.9950.0390.0851.15681.5
2.17-2.2740.07559920.9950.0390.0851.41981.8
2.27-2.393.90.07560870.9940.0380.0851.6982.7
2.39-2.543.90.07661890.9940.0390.0852.10184
2.54-2.743.70.07266140.9940.0380.0822.44289.9
2.74-3.013.60.06670770.9950.0340.0752.59895.3
3.01-3.453.70.04973600.9980.0260.0552.20898.8
3.45-4.343.90.03174470.9980.0170.0361.60499
4.34-503.80.02773730.9990.0150.0311.27393.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4XCA

4xca


Resolution: 1.6→35.352 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 6299 4.96 %
Rwork0.2216 120599 -
obs0.2232 126898 86.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.64 Å2 / Biso mean: 22.3972 Å2 / Biso min: 6.79 Å2
Refinement stepCycle: final / Resolution: 1.6→35.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8116 0 188 578 8882
Biso mean--20.22 25.46 -
Num. residues----1024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068540
X-RAY DIFFRACTIONf_angle_d1.10611625
X-RAY DIFFRACTIONf_chiral_restr0.0461313
X-RAY DIFFRACTIONf_plane_restr0.0051517
X-RAY DIFFRACTIONf_dihedral_angle_d14.573130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5933-1.61140.31031830.27093594377778
1.6114-1.63030.32092090.26113850405984
1.6303-1.65020.28081970.24553797399483
1.6502-1.67110.28282020.24933871407383
1.6711-1.69310.25961970.24443826402384
1.6931-1.71630.34472170.25663868408584
1.7163-1.74080.31792190.25313876409584
1.7408-1.76680.27181730.24663902407584
1.7668-1.79440.30482110.25573934414584
1.7944-1.82380.28541940.2393856405084
1.8238-1.85520.262050.24723919412484
1.8552-1.8890.30661840.24683869405384
1.889-1.92530.24761770.24093940411784
1.9253-1.96460.27261850.24353822400783
1.9646-2.00730.28142360.24563856409283
2.0073-2.0540.28542070.23753729393682
2.054-2.10540.27761810.23663872405382
2.1054-2.16230.30051710.23483790396182
2.1623-2.22590.261930.23353786397982
2.2259-2.29770.27951980.23073883408183
2.2977-2.37980.24811990.23343835403483
2.3798-2.47510.27282030.22943894409784
2.4751-2.58770.27192450.23424006425186
2.5877-2.72410.24762080.23724264447291
2.7241-2.89470.26122580.23784414467294
2.8947-3.11810.27652280.22934621484998
3.1181-3.43160.25282810.22044646492799
3.4316-3.92760.21712490.19854708495799
3.9276-4.94620.20162630.16874717498098
4.9462-35.36070.19662260.18564654488092

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