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- PDB-7qwi: Vanadate complex of the vanadium-dependent bromoperoxidase from C... -

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Basic information

Entry
Database: PDB / ID: 7qwi
TitleVanadate complex of the vanadium-dependent bromoperoxidase from Corallina pilulifera
ComponentsVanadium-dependent bromoperoxidase
KeywordsOXIDOREDUCTASE / Vanadium protein / halogen binding / haloperoxidase.
Function / homology
Function and homology information


bromide peroxidase / bromide peroxidase activity / metal ion binding
Similarity search - Function
Bromoperoxidase/chloroperoxidase C-terminal / : / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / BROMIDE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / VANADATE ION / Vanadium-dependent bromoperoxidase
Similarity search - Component
Biological speciesCorallina pilulifera (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 25, 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)269,20393
Polymers262,4594
Non-polymers6,74489
Water53,1802952
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)807,608279
Polymers787,37612
Non-polymers20,232267
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x+1/2,-y+3/21
crystal symmetry operation11_466y-1/2,-z+3/2,-x+11
Buried area140960 Å2
ΔGint-417 kcal/mol
Surface area203250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.601, 199.601, 199.601
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11DDD-601-

NA

21BBB-1353-

HOH

31BBB-1392-

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: 65614.672 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 , 9 types, 3041 molecules

#2: Chemical
ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: VO4 / 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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H12NO3
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2952 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM Tris-H2SO4, pH 6.8, 0.4M KBr, 1mM Na3VO4, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.92 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.15→14.965 Å / Num. obs: 142571 / % possible obs: 96.4 % / Redundancy: 4.9 % / CC1/2: 0.977 / Rsym value: 0.155 / Net I/σ(I): 8.1
Reflection shellResolution: 2.15→2.19 Å / Num. unique obs: 2680 / CC1/2: 0.809 / Rsym value: 0.502

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Processing

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

1up8


Resolution: 2.15→14.965 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.131 / SU B: 4.775 / SU ML: 0.122 / Average fsc free: 0.9389 / Average fsc work: 0.9526 / Cross valid method: FREE R-VALUE / ESU R: 0.22 / ESU R Free: 0.173 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1945 7104 5.022 %
Rwork0.1443 134358 -
all0.147 --
obs-141462 98.889 %
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: 19.248 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.15→14.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18448 0 365 2952 21765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01219633
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.65226648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08152519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49823.481043
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.457153119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.83615112
X-RAY DIFFRACTIONr_chiral_restr0.0910.22552
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215156
X-RAY DIFFRACTIONr_nbd_refined0.2080.210469
X-RAY DIFFRACTIONr_nbtor_refined0.3120.213468
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.22388
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.220
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.2180
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.289
X-RAY DIFFRACTIONr_mcbond_it3.2484.4789696
X-RAY DIFFRACTIONr_mcangle_it3.8097.48412152
X-RAY DIFFRACTIONr_scbond_it5.5825.0459936
X-RAY DIFFRACTIONr_scangle_it6.4698.05914432
X-RAY DIFFRACTIONr_lrange_it6.98533.41890367
X-RAY DIFFRACTIONr_ncsr_local_group_10.0540.0520441
X-RAY DIFFRACTIONr_ncsr_local_group_20.0440.0520482
X-RAY DIFFRACTIONr_ncsr_local_group_30.0520.0520448
X-RAY DIFFRACTIONr_ncsr_local_group_40.0530.0520347
X-RAY DIFFRACTIONr_ncsr_local_group_50.050.0520410
X-RAY DIFFRACTIONr_ncsr_local_group_60.0520.0520391
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.053560.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.053560.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.043730.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.043730.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.052340.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.052340.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.052510.05009
48CCCX-RAY DIFFRACTIONLocal ncs0.052510.05009
59BBBX-RAY DIFFRACTIONLocal ncs0.050290.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.050290.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.052250.05009
612DDDX-RAY DIFFRACTIONLocal ncs0.052250.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2060.2495290.1879926X-RAY DIFFRACTION99.6189
2.206-2.2660.2245310.1759679X-RAY DIFFRACTION99.4255
2.266-2.3320.2434900.179405X-RAY DIFFRACTION99.3574
2.332-2.4040.2124950.1559090X-RAY DIFFRACTION99.3676
2.404-2.4830.2314630.1588896X-RAY DIFFRACTION99.2997
2.483-2.570.2244380.1578577X-RAY DIFFRACTION99.2951
2.57-2.6670.2374340.1528272X-RAY DIFFRACTION99.0218
2.667-2.7760.2184390.1537886X-RAY DIFFRACTION98.9422
2.776-2.8990.234100.1517650X-RAY DIFFRACTION98.9321
2.899-3.040.2253510.1587244X-RAY DIFFRACTION98.4701
3.04-3.2050.1913760.1586970X-RAY DIFFRACTION99.1898
3.205-3.3990.2013750.1566619X-RAY DIFFRACTION99.5445
3.399-3.6340.1773260.1346183X-RAY DIFFRACTION99.3134
3.634-3.9240.1662930.1225776X-RAY DIFFRACTION98.9726
3.924-4.2990.1472840.1075294X-RAY DIFFRACTION98.6733
4.299-4.8060.1262340.1014857X-RAY DIFFRACTION99.0082
4.806-5.5480.1422290.1074304X-RAY DIFFRACTION99.4733
5.548-6.7920.1551980.1343668X-RAY DIFFRACTION99.6906
6.792-9.5940.1541440.142875X-RAY DIFFRACTION99.7357
9.594-14.9650.172650.1511187X-RAY DIFFRACTION72.0783

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