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- PDB-5j4r: WELO5 SMALL MOLECULE HALOGENASE WITH NI(II) AND 2-OXOGLUTARATE -

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Basic information

Entry
Database: PDB / ID: 5j4r
TitleWELO5 SMALL MOLECULE HALOGENASE WITH NI(II) AND 2-OXOGLUTARATE
ComponentsWelO5
KeywordsHYDROLASE / 2-oxoglutarate and iron dependendent halogenase / small molecule halogenase
Function / homologyCarrier-protein-independent halogenase WelO5 / metal ion binding / 2-OXOGLUTARIC ACID / NICKEL (II) ION / WelO5
Function and homology information
Biological speciesHapalosiphon welwitschii UTEX B 1830 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsMcDonough, M.A. / Gallimore, E. / Clifton, I.J. / Schofield, C.J.
CitationJournal: To Be Published
Title: WELO5 SMALL MOLECULE HALOGENASE WITH NI(II) AND 2-OXOGLUTARATE
Authors: Gallimore, E. / McDonough, M.A. / Clifton, I.J. / Schofield, C.J.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WelO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7633
Polymers32,5581
Non-polymers2052
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-12 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.030, 102.770, 123.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein WelO5


Mass: 32557.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hapalosiphon welwitschii UTEX B 1830 (bacteria)
Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A067YX61
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1 part Well solution: 100mM 2-(N-morpholino)ethanesulfonic acid pH 5.5, 100 mM sodium chloride, 22% polyethylene glycol 6000 added to 1 part protein 27 mg/mL, 5 mM nickel chloride, 5 mM 2- ...Details: 1 part Well solution: 100mM 2-(N-morpholino)ethanesulfonic acid pH 5.5, 100 mM sodium chloride, 22% polyethylene glycol 6000 added to 1 part protein 27 mg/mL, 5 mM nickel chloride, 5 mM 2-oxoglutarate, 20 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, 5mM (6aS,9S,10aS)-6,6,9-trimethyl-9-vinyl-6a,7,8,10a-tetrahydro-5H-indeno[2,1-b]indol-10-one

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.56→47.98 Å / Num. obs: 83245 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 20.8 % / Biso Wilson estimate: 21.88 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Net I/σ(I): 29.7
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 1.5 / % possible all: 51.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX(dev_2328: ???)refinement
XSCALEdata scaling
SHELXphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.65→47.976 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1602 3430 4.55 %
Rwork0.1376 --
obs0.1386 75312 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→47.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 11 246 2439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182299
X-RAY DIFFRACTIONf_angle_d1.4743125
X-RAY DIFFRACTIONf_dihedral_angle_d14.61379
X-RAY DIFFRACTIONf_chiral_restr0.089336
X-RAY DIFFRACTIONf_plane_restr0.011415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.67360.29171180.24512430X-RAY DIFFRACTION79
1.6736-1.69860.28421340.21722713X-RAY DIFFRACTION88
1.6986-1.72510.22261380.19592854X-RAY DIFFRACTION94
1.7251-1.75340.20991420.1812914X-RAY DIFFRACTION95
1.7534-1.78360.21211320.16242909X-RAY DIFFRACTION96
1.7836-1.81610.22321400.16122963X-RAY DIFFRACTION97
1.8161-1.8510.21261400.15393013X-RAY DIFFRACTION98
1.851-1.88880.17771590.15013034X-RAY DIFFRACTION98
1.8888-1.92990.15831410.14883053X-RAY DIFFRACTION98
1.9299-1.97470.16621410.14313020X-RAY DIFFRACTION99
1.9747-2.02410.15571430.14033050X-RAY DIFFRACTION99
2.0241-2.07890.18811440.13753087X-RAY DIFFRACTION99
2.0789-2.140.18271510.13543008X-RAY DIFFRACTION99
2.14-2.20910.14691530.1333076X-RAY DIFFRACTION100
2.2091-2.28810.16011450.13353120X-RAY DIFFRACTION100
2.2881-2.37970.14151360.12713032X-RAY DIFFRACTION100
2.3797-2.4880.15231600.12973109X-RAY DIFFRACTION100
2.488-2.61910.18241430.13013026X-RAY DIFFRACTION100
2.6191-2.78320.15251480.13683084X-RAY DIFFRACTION100
2.7832-2.99810.16181370.13483086X-RAY DIFFRACTION100
2.9981-3.29970.18781450.13953075X-RAY DIFFRACTION100
3.2997-3.7770.16151430.13093060X-RAY DIFFRACTION100
3.777-4.7580.10931500.11183090X-RAY DIFFRACTION100
4.758-47.99670.1451470.14853076X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.41350.3401-0.92391.0361-0.50292.94590.0378-0.1520.0261-0.0002-0.0332-0.0669-0.17320.288-0.00660.1548-0.02140.00240.1423-0.00840.18338.096719.655846.4515
21.840.4213-0.13441.63260.49412.5742-0.03430.003-0.1804-0.1180.0794-0.19730.0970.4199-0.06210.13360.0180.0160.15430.02270.148210.306210.625538.4106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 150 )
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 290 )

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