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- PDB-7qyy: Vanadium-dependent bromoperoxidase from Corallina pilulifera in c... -

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Basic information

Entry
Database: PDB / ID: 7qyy
TitleVanadium-dependent bromoperoxidase from Corallina pilulifera in complex with chloride
ComponentsVanadium-dependent bromoperoxidase
KeywordsOXIDOREDUCTASE / Vanadium protein / halogen binding / haloperoxidase.
Function / homologybromide peroxidase / bromide peroxidase activity / Bromoperoxidase/chloroperoxidase C-terminal / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / metal ion binding / PHOSPHATE ION / Vanadium-dependent bromoperoxidase
Function and homology information
Biological speciesCorallina pilulifera (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsIsupov, M.N. / Mitchell, D. / Littelchild, J.A. / Garcia-Rodriguez, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: R396W mutant of the vanadium-dependent bromoperoxidase from Corallina pilulifera
Authors: Isupov, M.N. / Mitchell, D. / Littelchild, J.A. / Garcia-Rodriguez, E.
History
DepositionJan 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Vanadium-dependent bromoperoxidase
BBB: Vanadium-dependent bromoperoxidase
CCC: Vanadium-dependent bromoperoxidase
DDD: Vanadium-dependent bromoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,059103
Polymers261,3764
Non-polymers7,68399
Water57,9003214
1
AAA: Vanadium-dependent bromoperoxidase
BBB: Vanadium-dependent bromoperoxidase
CCC: Vanadium-dependent bromoperoxidase
DDD: Vanadium-dependent bromoperoxidase
hetero molecules

AAA: Vanadium-dependent bromoperoxidase
BBB: Vanadium-dependent bromoperoxidase
CCC: Vanadium-dependent bromoperoxidase
DDD: Vanadium-dependent bromoperoxidase
hetero molecules

AAA: Vanadium-dependent bromoperoxidase
BBB: Vanadium-dependent bromoperoxidase
CCC: Vanadium-dependent bromoperoxidase
DDD: Vanadium-dependent bromoperoxidase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 807 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)807,177309
Polymers784,12712
Non-polymers23,050297
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area176580 Å2
ΔGint-1790 kcal/mol
Surface area190960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.115, 182.115, 177.602
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11BBB-1457-

HOH

21CCC-1484-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74BBB
84CCC
95BBB
105DDD
116CCC
126DDD

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 2 - 598 / Label seq-ID: 2 - 598

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AAAA
211BBBB
322AAAA
422CCCC
533AAAA
633DDDD
744BBBB
844CCCC
955BBBB
1055DDDD
1166CCCC
1266DDDD

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
Vanadium-dependent bromoperoxidase / V-BPO / Vanadium haloperoxidase


Mass: 65343.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corallina pilulifera (eukaryote) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O81959, bromide peroxidase

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Non-polymers , 6 types, 3313 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 65 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3214 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HBr, pH 7.4, 1.3M ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8482 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8482 Å / Relative weight: 1
ReflectionResolution: 1.999→99 Å / Num. obs: 218890 / % possible obs: 97.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.2
Reflection shellResolution: 1.999→2.07 Å / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 20725

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1up8

1up8


Resolution: 1.999→19.962 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.556 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.134 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1928 10625 5.015 %
Rwork0.146 201248 -
all0.148 --
obs-211873 94.254 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 24.081 Å2
Baniso -1Baniso -2Baniso -3
1-0.283 Å20.141 Å20 Å2
2--0.283 Å20 Å2
3----0.918 Å2
Refinement stepCycle: LAST / Resolution: 1.999→19.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18420 0 460 3214 22094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01219940
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.63127131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19352601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34523.5211068
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.298153213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.02915112
X-RAY DIFFRACTIONr_chiral_restr0.1180.22595
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215400
X-RAY DIFFRACTIONr_nbd_refined0.2150.211006
X-RAY DIFFRACTIONr_nbtor_refined0.3230.213794
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.22570
X-RAY DIFFRACTIONr_metal_ion_refined0.290.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.2328
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.2130
X-RAY DIFFRACTIONr_mcbond_it5.3135.5649826
X-RAY DIFFRACTIONr_mcangle_it5.5589.24812320
X-RAY DIFFRACTIONr_scbond_it8.6516.18610114
X-RAY DIFFRACTIONr_scangle_it9.2579.94614703
X-RAY DIFFRACTIONr_lrange_it9.08141.91293503
X-RAY DIFFRACTIONr_ncsr_local_group_10.0530.0520607
X-RAY DIFFRACTIONr_ncsr_local_group_20.0540.0520593
X-RAY DIFFRACTIONr_ncsr_local_group_30.0490.0520661
X-RAY DIFFRACTIONr_ncsr_local_group_40.0550.0520570
X-RAY DIFFRACTIONr_ncsr_local_group_50.0490.0520636
X-RAY DIFFRACTIONr_ncsr_local_group_60.0540.0520693
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.053090.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.053090.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.054090.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.054090.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.049310.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.049310.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.054940.05009
48CCCX-RAY DIFFRACTIONLocal ncs0.054940.05009
59BBBX-RAY DIFFRACTIONLocal ncs0.049120.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.049120.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.054130.05009
612DDDX-RAY DIFFRACTIONLocal ncs0.054130.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.0510.3087670.26114396X-RAY DIFFRACTION91.5088
2.051-2.1070.2697310.21914368X-RAY DIFFRACTION93.5328
2.107-2.1680.2687220.19914070X-RAY DIFFRACTION93.6736
2.168-2.2350.2557340.19313584X-RAY DIFFRACTION94.0118
2.235-2.3080.2287030.17713133X-RAY DIFFRACTION93.3855
2.308-2.3890.2236940.17512754X-RAY DIFFRACTION94.0485
2.389-2.480.2136300.1612400X-RAY DIFFRACTION94.2087
2.48-2.5810.2076080.15511966X-RAY DIFFRACTION94.5627
2.581-2.6960.2146150.14711417X-RAY DIFFRACTION94.2282
2.696-2.8270.1975880.14910884X-RAY DIFFRACTION93.9789
2.827-2.980.1995910.14510404X-RAY DIFFRACTION94.6865
2.98-3.1610.2025780.1429830X-RAY DIFFRACTION94.7905
3.161-3.3790.1855180.1339338X-RAY DIFFRACTION95.1627
3.379-3.6490.1594160.1188783X-RAY DIFFRACTION95.7431
3.649-3.9970.144330.1078026X-RAY DIFFRACTION95.7442
3.997-4.4690.1213450.0877411X-RAY DIFFRACTION96.1925
4.469-5.160.1233390.0896506X-RAY DIFFRACTION96.9959
5.16-6.3170.1582920.1235587X-RAY DIFFRACTION97.8691
6.317-8.9270.1532240.1324352X-RAY DIFFRACTION98.5145
8.927-19.9620.211970.2192041X-RAY DIFFRACTION81.9157

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