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- PDB-5iqv: WelO5 bound to Fe, Cl, 2-oxoglutarate, 12-epifischerindole U, and... -

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Basic information

Entry
Database: PDB / ID: 5iqv
TitleWelO5 bound to Fe, Cl, 2-oxoglutarate, 12-epifischerindole U, and nitric oxide
ComponentsWelO5
KeywordsOXIDOREDUCTASE / etalloenzyme halogenase 2-oxoglutarate nitric oxide
Function / homologymetal ion binding / Chem-6CU / 2-OXOGLUTARIC ACID / : / NITRIC OXIDE / WelO5
Function and homology information
Biological speciesHapalosiphon welwitschii UTEX B 1830 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMitchell, A.J. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100011 United States
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural basis for halogenation by iron- and 2-oxo-glutarate-dependent enzyme WelO5.
Authors: Mitchell, A.J. / Zhu, Q. / Maggiolo, A.O. / Ananth, N.R. / Hillwig, M.L. / Liu, X. / Boal, A.K.
History
DepositionMar 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Apr 13, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _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
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WelO5
B: WelO5
C: WelO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,28117
Polymers106,5903
Non-polymers1,69214
Water2,828157
1
A: WelO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1046
Polymers35,5301
Non-polymers5745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WelO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1046
Polymers35,5301
Non-polymers5745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: WelO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0745
Polymers35,5301
Non-polymers5444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.729, 84.576, 142.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein WelO5


Mass: 35529.945 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hapalosiphon welwitschii UTEX B 1830 (bacteria)
Strain: UTEX B 1830 / Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: A0A067YX61

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Non-polymers , 6 types, 171 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-6CU / (6aS,9R,10R,10aS)-9-ethyl-10-isocyano-6,6,9-trimethyl-5,6,6a,7,8,9,10,10a-octahydroindeno[2,1-b]indole / 12-epi-fischerindole U


Mass: 306.445 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H26N2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1.99 Å3/Da / Density % sol: 38.3 % / Description: Long needles/rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.1 M Bis-tris pH 5.5, 0.1 M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35084 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.122 / Net I/av σ(I): 17.306 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.447.40.9711100
2.44-2.497.50.8941100
2.49-2.537.40.8011100
2.53-2.597.50.6911100
2.59-2.647.50.6251100
2.64-2.77.50.5571100
2.7-2.777.40.4721100
2.77-2.857.50.3921100
2.85-2.937.50.3331100
2.93-3.027.40.2851100
3.02-3.137.40.2111100
3.13-3.267.40.1741100
3.26-3.417.40.1411100
3.41-3.587.40.1121100
3.58-3.817.40.0941100
3.81-4.17.40.0671100
4.1-4.527.30.0461100
4.52-5.177.30.041100
5.17-6.517.20.0411100
6.51-506.70.032199.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IQS

5iqs


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.21 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.521 / ESU R Free: 0.264
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 1740 5 %RANDOM
Rwork0.2016 ---
obs0.2036 33111 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.68 Å2 / Biso mean: 40.284 Å2 / Biso min: 17.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6523 0 109 157 6789
Biso mean--39.51 37.9 -
Num. residues----827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196781
X-RAY DIFFRACTIONr_bond_other_d0.0010.026334
X-RAY DIFFRACTIONr_angle_refined_deg1.0031.9759193
X-RAY DIFFRACTIONr_angle_other_deg0.6943.00314576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50824.321324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1151110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.971539
X-RAY DIFFRACTIONr_chiral_restr0.0570.2986
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217706
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021587
X-RAY DIFFRACTIONr_mcbond_it1.0313.9963304
X-RAY DIFFRACTIONr_mcbond_other1.0313.9973301
X-RAY DIFFRACTIONr_mcangle_it1.855.9874117
LS refinement shellResolution: 2.4→2.432 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 107 -
Rwork0.276 2028 -
all-2135 -
obs--82.98 %

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