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- PDB-5trq: WELO5 SMALL MOLECULE HALOGENASE WITH NI(II) AND SUCCINATE -

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Basic information

Entry
Database: PDB / ID: 5trq
TitleWELO5 SMALL MOLECULE HALOGENASE WITH NI(II) AND SUCCINATE
ComponentsWelO5
KeywordsOXIDOREDUCTASE / Halogenase / 2-oxoglutarate and Fe(II)-dependent oxygenase
Function / homologyACETATE ION / NICKEL (II) ION / SUCCINIC ACID / WelO5
Function and homology information
Biological speciesHapalosiphon welwitschii UTEX B 1830 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsMcDonough, M.A. / Gallimore, E. / Clifton, I.J.
CitationJournal: To be published
Title: WELO5 SMALL MOLECULE HALOGENASE WITH NI(II) AND SUCCINATE
Authors: Gallimore, E.O. / McDonough, M.A. / Clifton, I.J. / Schofield, C.J.
History
DepositionOct 27, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / database_2 / pdbx_initial_refinement_model / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WelO5
B: WelO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,15316
Polymers65,1152
Non-polymers1,03814
Water9,188510
1
A: WelO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0588
Polymers32,5581
Non-polymers5007
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WelO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0958
Polymers32,5581
Non-polymers5387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.063, 46.066, 74.437
Angle α, β, γ (deg.)91.770, 90.540, 108.710
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein WelO5


Mass: 32557.744 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 524 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-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M MES PH6.0, 0.2M CALCIUM ACETATE, 20% (W/V) POLYETHYLENE GLYCOL 8000, PROTEIN 27 MG/ML, 5MM NICKEL CHLORIDE, 5MM SUCCINATE, 20 MM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.3→38.22 Å / Num. obs: 135629 / % possible obs: 95.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.2
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.64 / % possible all: 92.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.25 Å38.22 Å
Translation7.25 Å38.22 Å

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J4R

5j4r


Resolution: 1.3→38.217 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.5
RfactorNum. reflection% reflection
Rfree0.2072 6550 4.92 %
Rwork0.1875 --
obs0.1885 133078 93.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.8 Å2 / Biso mean: 26.3059 Å2 / Biso min: 4.49 Å2
Refinement stepCycle: final / Resolution: 1.3→38.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 54 511 4965
Biso mean--36.47 35.23 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144791
X-RAY DIFFRACTIONf_angle_d1.2056553
X-RAY DIFFRACTIONf_chiral_restr0.091719
X-RAY DIFFRACTIONf_plane_restr0.008869
X-RAY DIFFRACTIONf_dihedral_angle_d14.7011816
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 (%)
1.3-1.31480.3992260.37993828405484
1.3148-1.33020.39342170.38283813403086
1.3302-1.34650.37721990.37264042424188
1.3465-1.36350.41431840.36123991417588
1.3635-1.38150.36132090.35014011422089
1.3815-1.40040.33942330.33934017425090
1.4004-1.42040.37432140.33954087430191
1.4204-1.44160.38752320.33484205443792
1.4416-1.46410.33271760.33194114429091
1.4641-1.48810.33282010.31564261446292
1.4881-1.51380.381800.29314123430393
1.5138-1.54130.30682020.27294289449193
1.5413-1.5710.28181970.26774158435593
1.571-1.6030.29022240.25154260448494
1.603-1.63790.28212060.24594299450594
1.6379-1.6760.23981930.22384292448595
1.676-1.71790.23581880.21524288447695
1.7179-1.76430.22982190.20144295451495
1.7643-1.81630.2412160.19484282449895
1.8163-1.87490.2392510.18694257450895
1.8749-1.94190.17732430.16444276451995
1.9419-2.01960.17192110.15774384459596
2.0196-2.11150.17862230.16324348457196
2.1115-2.22290.22292740.15624313458797
2.2229-2.36210.16261920.15284357454996
2.3621-2.54440.18562430.15534377462097
2.5444-2.80040.16331930.15914377457097
2.8004-3.20550.17972590.15184359461897
3.2055-4.03790.15622730.14444377465098
4.0379-38.23370.17522720.16154448472099
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)
11.4503-0.2597-0.31080.96340.84073.2104-0.1395-0.2609-0.11550.2030.08950.03020.1341-0.13190.03380.18520.01330.00830.17170.04070.1312-40.647813.651627.9111
21.7715-0.0768-0.62290.76310.30581.5645-0.0906-0.2169-0.00710.11020.088-0.13920.03260.1960.0160.10310.0034-0.01980.1086-0.0070.0998-32.280218.164118.5294
31.4863-0.5289-0.85031.26180.25843.19480.0970.3119-0.1271-0.1948-0.17740.11070.1791-0.04940.05360.16420.0171-0.03110.2025-0.02910.1438-51.795121.8887-16.3336
40.9259-0.3958-0.44821.65420.58231.59440.09170.18250.114-0.1635-0.11860.0493-0.1642-0.08720.03020.10340.0030.00050.10640.02030.0957-50.526730.9947-7.151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 150 )A8 - 150
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 290 )A151 - 290
3X-RAY DIFFRACTION3chain 'B' and (resid 8 through 150 )B8 - 150
4X-RAY DIFFRACTION4chain 'B' and (resid 151 through 290 )B151 - 290

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