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

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Basic information

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


q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / NICKEL (II) ION / Putative oxidase/hydroxylase
Similarity search - Component
Biological speciesStreptomyces hygroscopicus subsp. hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.295 Å
AuthorsMcCulloch, K.M. / McCranie, E.K. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32 HL007751 United States
American Heart Association12GRNT11920011 United States
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 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
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.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 / _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)117,26616
Polymers115,9264
Non-polymers1,34012
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16720 Å2
ΔGint-188 kcal/mol
Surface area35970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.399, 112.044, 177.803
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

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Protein , 1 types, 4 molecules ABCD

#1: Protein
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

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Non-polymers , 5 types, 511 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


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


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, 50 mM CsCl, 30% Jeffamine M-600. Sample was pre-incubated with 3 mM 2-oxoglutarate for 30 minutes.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-D11.485
SYNCHROTRONAPS 21-ID-F20.979
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.4851
20.9791
ReflectionRedundancy: 7.3 % / Number: 168858 / Rmerge(I) obs: 0.105 / Χ2: 2.59 / D res high: 2.95 Å / D res low: 50 Å / Num. obs: 23283 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.355010.0632.6247
5.046.3510.0832.8127.4
4.415.0410.0872.8847.4
44.4110.1013.0047.3
3.72410.1163.6786.7
3.53.7210.162.8216.8
3.323.510.152.677.4
3.183.3210.2022.1717.5
3.063.1810.2671.7977.6
2.953.0610.331.6097.5
ReflectionResolution: 2.3→50 Å / Num. obs: 46741 / % possible obs: 96.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 32.73 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.037 / Rrim(I) all: 0.081 / Χ2: 1.265 / Net I/av σ(I): 21.085 / Net I/σ(I): 13.2 / Num. measured all: 204918
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.344.40.23423560.9790.1160.2620.93597.8
2.34-2.384.40.19823430.9820.0980.2220.92298.6
2.38-2.434.40.18123320.9820.090.2031.00297.2
2.43-2.484.40.16523450.9840.0830.1851.00199.3
2.48-2.534.40.15123760.9870.0760.171.03198.9
2.53-2.594.40.13423920.9880.0670.151.1199
2.59-2.664.40.11723950.990.060.1321.18599.3
2.66-2.734.50.10623580.9930.0530.1191.18899.4
2.73-2.814.50.09624240.9920.0490.1091.26799.6
2.81-2.94.50.08723520.9940.0450.0981.19199.5
2.9-34.50.07924370.9930.0410.091.2599.9
3-3.124.50.07424140.9950.0380.0831.365100
3.12-3.264.50.07624050.9930.040.0861.413100
3.26-3.444.50.07624110.9920.040.0861.69199.1
3.44-3.6540.08819730.9850.0480.1011.77881.2
3.65-3.933.70.11418810.9680.0640.1322.31577.2
3.93-4.334.30.06721380.9930.0350.0761.9486.6
4.33-4.954.40.04824390.9960.0250.0551.41398.3
4.95-6.244.50.03724690.9980.0190.0420.99398.4
6.24-504.20.03725010.9970.020.0430.91493.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.295→40.713 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2363 3991 8.56 %
Rwork0.1755 42652 -
obs0.1808 46643 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.14 Å2 / Biso mean: 30.7862 Å2 / Biso min: 13.38 Å2
Refinement stepCycle: final / Resolution: 2.295→40.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7985 0 55 499 8539
Biso mean--37.47 33.08 -
Num. residues----1005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088202
X-RAY DIFFRACTIONf_angle_d1.09111120
X-RAY DIFFRACTIONf_chiral_restr0.0421218
X-RAY DIFFRACTIONf_plane_restr0.0051476
X-RAY DIFFRACTIONf_dihedral_angle_d14.7033048
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2951-2.32210.31821350.20191386152191
2.3221-2.35040.30191210.191485160699
2.3504-2.38010.25041370.18681496163398
2.3801-2.41140.29291300.18671464159497
2.4114-2.44450.26461410.18431499164099
2.4445-2.47940.29051340.190514901624100
2.4794-2.51640.32341290.19541488161799
2.5164-2.55570.32971490.18251512166199
2.5557-2.59760.27111220.18991500162299
2.5976-2.64240.30791600.18781502166299
2.6424-2.69040.28031550.19231498165399
2.6904-2.74220.30771510.192514881639100
2.7422-2.79810.31891600.195115111671100
2.7981-2.8590.25561370.188914931630100
2.859-2.92540.26941180.191815521670100
2.9254-2.99860.25341460.172315291675100
2.9986-3.07960.26831390.18114961635100
3.0796-3.17020.25841450.185315401685100
3.1702-3.27250.24121450.179915341679100
3.2725-3.38940.25881460.18091506165299
3.3894-3.5250.22411390.18121529166899
3.525-3.68540.281970.22511117121472
3.6854-3.87950.21251250.18041326145185
3.8795-4.12240.21970.1464980107764
4.1224-4.44030.17191440.13171527167199
4.4403-4.88650.15441470.12341529167698
4.8865-5.5920.16731460.14141543168999
5.592-7.03940.19911460.17541566171298
7.0394-40.7190.22591500.19911566171693

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