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- PDB-7qvw: R396W mutant of the vanadium-dependent bromoperoxidase from Coral... -

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Basic information

Entry
Database: PDB / ID: 7qvw
TitleR396W mutant of the vanadium-dependent bromoperoxidase from Corallina pilulifera
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 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / PHOSPHATE ION / Vanadium-dependent bromoperoxidase
Function and homology information
Biological speciesCorallina pilulifera (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.922 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 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 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)269,29591
Polymers262,1234
Non-polymers7,17287
Water56,6933147
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
  • 808 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)807,885273
Polymers786,36912
Non-polymers21,516261
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 area171770 Å2
ΔGint-1326 kcal/mol
Surface area190680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.148, 182.148, 177.186
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-1435-

HOH

21BBB-1456-

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: 65530.762 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, 3234 molecules

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


Mass: 94.971 Da / Num. of mol.: 10 / 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
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 62 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3147 / 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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl and 2 M ammonium dihydrogen phosphate at pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.9076 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 1.92→49.603 Å / Num. obs: 246831 / % possible obs: 97.8 % / Redundancy: 5.6 % / CC1/2: 0.997 / Net I/σ(I): 16.5
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 3 % / Num. unique obs: 10100 / CC1/2: 0.38 / % possible all: 80.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DENZOdata reduction
XDSdata reduction
SCALEPACKdata scaling
XSCALEdata scaling
MOLREPphasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UP8

1up8


Resolution: 1.922→49.603 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.136 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.111 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1855 2460 1.004 %
Rwork0.1531 242490 -
all0.1531 --
obs-244950 96.98 %
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: 30.913 Å2
Baniso -1Baniso -2Baniso -3
1-0.549 Å20.275 Å20 Å2
2--0.549 Å20 Å2
3----1.781 Å2
Refinement stepCycle: LAST / Resolution: 1.922→49.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18440 0 444 3147 22031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01220387
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.63527830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13452720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5423.6821070
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.916153317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91715108
X-RAY DIFFRACTIONr_chiral_restr0.1020.22671
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215756
X-RAY DIFFRACTIONr_nbd_refined0.2190.211496
X-RAY DIFFRACTIONr_nbtor_refined0.3220.213996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.22722
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2710.2345
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.2125
X-RAY DIFFRACTIONr_mcbond_it4.9047.4469983
X-RAY DIFFRACTIONr_mcangle_it5.29212.44412549
X-RAY DIFFRACTIONr_scbond_it8.0198.08210404
X-RAY DIFFRACTIONr_scangle_it8.24813.1515123
X-RAY DIFFRACTIONr_lrange_it8.25343.45434552
X-RAY DIFFRACTIONr_ncsr_local_group_10.0580.0520956
X-RAY DIFFRACTIONr_ncsr_local_group_20.060.0520970
X-RAY DIFFRACTIONr_ncsr_local_group_30.0570.0521034
X-RAY DIFFRACTIONr_ncsr_local_group_40.060.0520970
X-RAY DIFFRACTIONr_ncsr_local_group_50.0540.0521129
X-RAY DIFFRACTIONr_ncsr_local_group_60.0610.0521135
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.05850.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.05850.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.060050.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.060050.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.057030.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.057030.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.060320.05009
48CCCX-RAY DIFFRACTIONLocal ncs0.060320.05009
59BBBX-RAY DIFFRACTIONLocal ncs0.054220.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.054220.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.061050.05009
612DDDX-RAY DIFFRACTIONLocal ncs0.061050.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.922-1.9720.3981480.36414712X-RAY DIFFRACTION79.781
1.972-2.0260.2981640.24617948X-RAY DIFFRACTION99.7412
2.026-2.0840.2211970.20417454X-RAY DIFFRACTION99.9321
2.084-2.1480.2631530.19616983X-RAY DIFFRACTION99.8543
2.148-2.2190.2411610.19716456X-RAY DIFFRACTION99.7239
2.219-2.2970.2081770.17915827X-RAY DIFFRACTION99.7258
2.297-2.3830.2311750.17815329X-RAY DIFFRACTION99.6849
2.383-2.4810.2171550.16414764X-RAY DIFFRACTION99.7593
2.481-2.5910.181420.15714179X-RAY DIFFRACTION99.7562
2.591-2.7170.1741270.14213529X-RAY DIFFRACTION99.6207
2.717-2.8640.1851330.14112838X-RAY DIFFRACTION99.5166
2.864-3.0380.1721340.15312133X-RAY DIFFRACTION99.1113
3.038-3.2480.1911180.1511231X-RAY DIFFRACTION97.8953
3.248-3.5080.152930.1310213X-RAY DIFFRACTION95.5675
3.508-3.8420.154830.1239268X-RAY DIFFRACTION93.8667
3.842-4.2960.132960.1038246X-RAY DIFFRACTION92.658
4.296-4.960.141680.0987370X-RAY DIFFRACTION93.5715
4.96-6.0730.148580.1356582X-RAY DIFFRACTION98.3267
6.073-8.5820.138480.1424855X-RAY DIFFRACTION93.9812
8.582-49.60.181300.1742573X-RAY DIFFRACTION88.9915

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