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- PDB-7qw3: R396W mutant of the vanadium-dependent bromoperoxidase from Coral... -

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Basic information

Entry
Database: PDB / ID: 7qw3
TitleR396W mutant of the vanadium-dependent bromoperoxidase from Corallina pilulifera in complex with Br ion.
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 / BROMIDE ION / PHOSPHATE ION / Vanadium-dependent bromoperoxidase
Function and homology information
Biological speciesCorallina pilulifera (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 24, 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)268,12377
Polymers262,1234
Non-polymers6,00073
Water66,6013697
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


Theoretical massNumber of molelcules
Total (without water)804,370231
Polymers786,36912
Non-polymers18,000219
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 area158260 Å2
ΔGint-1161 kcal/mol
Surface area192980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.484, 182.484, 177.592
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-1547-

HOH

21CCC-707-

HOH

31CCC-1395-

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
221BBBB
332AAAA
442CCCC
553AAAA
663DDDD
774BBBB
884CCCC
995BBBB
10105DDDD
11116CCCC
12126DDDD

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, 3770 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3697 / 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: 3.26 Å3/Da / Density % sol: 62.23 %
Crystal growTemperature: 293 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: 0.9763 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.78→29.996 Å / Num. obs: 309584 / % possible obs: 97 % / Redundancy: 2.5 % / CC1/2: 0.993 / Rsym value: 0.048 / Net I/σ(I): 13.2
Reflection shellResolution: 1.78→1.81 Å / Num. unique obs: 14892 / CC1/2: 0.69 / Rsym value: 0.397

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Processing

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

1up8


Resolution: 1.78→29.996 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.96 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.089 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1713 15613 5.046 %
Rwork0.1428 293781 -
all0.144 --
obs-309394 96.871 %
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: 19.869 Å2
Baniso -1Baniso -2Baniso -3
1-0.262 Å20.131 Å20 Å2
2--0.262 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.78→29.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18440 0 304 3697 22441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01220409
X-RAY DIFFRACTIONr_angle_refined_deg1.541.63727984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.952772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66123.8121086
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.749153356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91315108
X-RAY DIFFRACTIONr_chiral_restr0.1010.22709
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215952
X-RAY DIFFRACTIONr_nbd_refined0.2120.211238
X-RAY DIFFRACTIONr_nbtor_refined0.3210.214052
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.22961
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2250.2287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.2144
X-RAY DIFFRACTIONr_mcbond_it2.9834.29210038
X-RAY DIFFRACTIONr_mcangle_it3.5457.18312631
X-RAY DIFFRACTIONr_scbond_it4.9384.90710371
X-RAY DIFFRACTIONr_scangle_it5.7237.91615157
X-RAY DIFFRACTIONr_lrange_it6.60633.61996373
X-RAY DIFFRACTIONr_ncsr_local_group_10.0590.0521123
X-RAY DIFFRACTIONr_ncsr_local_group_20.0630.0521053
X-RAY DIFFRACTIONr_ncsr_local_group_30.0570.0521150
X-RAY DIFFRACTIONr_ncsr_local_group_40.0610.0520898
X-RAY DIFFRACTIONr_ncsr_local_group_50.0570.0521010
X-RAY DIFFRACTIONr_ncsr_local_group_60.0620.0521053
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.059280.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.059280.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.062590.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.062590.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.057380.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.057380.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.060620.05009
48CCCX-RAY DIFFRACTIONLocal ncs0.060620.05009
59BBBX-RAY DIFFRACTIONLocal ncs0.057110.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.057110.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.061960.05009
612DDDX-RAY DIFFRACTIONLocal ncs0.061960.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.8260.29411200.26521555X-RAY DIFFRACTION96.3336
1.826-1.8760.2411330.21321114X-RAY DIFFRACTION96.8862
1.876-1.9310.22711010.1920718X-RAY DIFFRACTION97.3758
1.931-1.990.20810650.17620197X-RAY DIFFRACTION97.9004
1.99-2.0550.19410800.16719608X-RAY DIFFRACTION98.243
2.055-2.1270.18610050.16119041X-RAY DIFFRACTION98.5982
2.127-2.2080.1769960.15318390X-RAY DIFFRACTION98.7771
2.208-2.2980.1839230.14917854X-RAY DIFFRACTION98.9878
2.298-2.40.1868880.14917090X-RAY DIFFRACTION98.9978
2.4-2.5170.1778720.14416306X-RAY DIFFRACTION99.1515
2.517-2.6530.1688130.13815499X-RAY DIFFRACTION98.7589
2.653-2.8140.1748030.13514523X-RAY DIFFRACTION98.3445
2.814-3.0080.1687440.13313571X-RAY DIFFRACTION97.5269
3.008-3.2490.1556970.12812531X-RAY DIFFRACTION96.7171
3.249-3.5590.1415960.11611431X-RAY DIFFRACTION95.5965
3.559-3.9790.1295470.10510181X-RAY DIFFRACTION94.064
3.979-4.5940.1174500.0938767X-RAY DIFFRACTION91.8028
4.594-5.6260.1373640.1117253X-RAY DIFFRACTION89.4434
5.626-7.9510.1542690.1425433X-RAY DIFFRACTION86.042
7.951-29.9960.1471470.1482719X-RAY DIFFRACTION78.0926

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