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- PDB-4zpi: Crystal Structure of HygX from Streptomyces hygroscopicus with ir... -

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Basic information

Entry
Database: PDB / ID: 4zpi
TitleCrystal Structure of HygX from Streptomyces hygroscopicus with iron bound
ComponentsPutative oxidase/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
: / SUCCINIC ACID / Putative oxidase/hydroxylase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus subsp. hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.504 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
DepositionMay 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 23, 2015Group: Database references
Revision 1.3Sep 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative oxidase/hydroxylase
B: Putative oxidase/hydroxylase
C: Putative oxidase/hydroxylase
D: Putative oxidase/hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,50411
Polymers115,9264
Non-polymers5787
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15310 Å2
ΔGint-97 kcal/mol
Surface area35540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.400, 108.989, 221.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative oxidase/hydroxylase


Mass: 28981.477 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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.6 M succinic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.739 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.739 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 40436 / % possible obs: 87.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 41.29 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.051 / Rrim(I) all: 0.107 / Χ2: 2.511 / Net I/av σ(I): 18.781 / Net I/σ(I): 10.8 / Num. measured all: 149043
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.30.58420260.7420.3470.6831.21489.8
2.54-2.593.20.49220770.8050.2940.5761.22391
2.59-2.643.30.41320240.8330.2430.4821.38889.7
2.64-2.693.30.37420310.8560.220.4361.51189.8
2.69-2.753.30.32120480.8860.1880.3741.63690.3
2.75-2.823.40.27320260.9170.160.3181.8489.5
2.82-2.893.40.25120490.9220.1460.2921.81289.8
2.89-2.963.40.2120410.9390.1230.2442.08590.6
2.96-3.053.50.18220430.960.1060.2112.19389.7
3.05-3.153.50.16420450.9690.0920.1892.46789.9
3.15-3.263.60.14720440.9670.0830.172.8289.5
3.26-3.393.70.11720660.9790.0650.1343.18189.2
3.39-3.553.80.09819940.9850.0530.1123.17788
3.55-3.733.90.08320080.9880.0450.0953.20687.7
3.73-3.9740.07920130.990.0420.093.37487.1
3.97-4.274.10.07619930.9890.040.0863.85486.3
4.27-4.74.10.06919800.9930.0350.0774.02584.9
4.7-5.384.30.05719860.9960.0280.0643.0184.4
5.38-6.784.40.05219850.9960.0260.0592.32882.7
6.78-504.30.04119570.9980.020.0462.31377.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.7phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XCA

4xca


Resolution: 2.504→48.674 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 3367 4.85 %
Rwork0.1704 66084 -
obs0.173 38440 79.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.28 Å2 / Biso mean: 39.4574 Å2 / Biso min: 17.21 Å2
Refinement stepCycle: final / Resolution: 2.504→48.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7851 0 28 140 8019
Biso mean--57.08 34.82 -
Num. residues----988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138048
X-RAY DIFFRACTIONf_angle_d1.1110889
X-RAY DIFFRACTIONf_chiral_restr0.0421194
X-RAY DIFFRACTIONf_plane_restr0.0051442
X-RAY DIFFRACTIONf_dihedral_angle_d14.4662974
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5041-2.53990.32641150.26852306242166
2.5399-2.57780.35971670.28322835300281
2.5778-2.61810.35541490.25552774292381
2.6181-2.6610.29491380.24962837297581
2.661-2.70690.23341090.22242901301082
2.7069-2.75610.31571360.23082846298282
2.7561-2.80910.28371410.22342829297081
2.8091-2.86640.29491560.22572860301682
2.8664-2.92880.30451250.22982830295582
2.9288-2.99690.29511520.2172855300782
2.9969-3.07180.27541390.20382829296882
3.0718-3.15480.27351410.20262834297582
3.1548-3.24770.24811520.19542814296681
3.2477-3.35250.2261810.1752762294381
3.3525-3.47230.23211750.16422767294280
3.4723-3.61120.19311570.16852761291879
3.6112-3.77550.24741180.16182710282879
3.7755-3.97450.2011440.14462727287178
3.9745-4.22340.20721430.13532709285277
4.2234-4.54930.14941300.12312695282577
4.5493-5.00660.14951270.1152666279377
5.0066-5.73010.16961280.13072674280277
5.7301-7.21560.1911380.1572636277476
7.2156-48.68290.19351060.14762627273375

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