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- PDB-7m1j: Crystal structure of dehaloperoxidase B in complex with 2,6-dibro... -

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Basic information

Entry
Database: PDB / ID: 7m1j
TitleCrystal structure of dehaloperoxidase B in complex with 2,6-dibromophenol
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / heme peroxidase / peroxygenase / heme cofactor / oxygen binding
Function / homology
Function and homology information


oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
2,6-bis(bromanyl)phenol / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.554 Å
AuthorsGhiladi, R.A. / de Serrano, V.S. / Malewschik, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Inorg.Biochem. / Year: 2022
Title: Bridging the functional gap between reactivity and inhibition in dehaloperoxidase B from Amphitrite ornata: Mechanistic and structural studies with 2,4- and 2,6-dihalophenols.
Authors: Malewschik, T. / Carey, L.M. / de Serrano, V. / Ghiladi, R.A.
History
DepositionMar 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehaloperoxidase B
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5988
Polymers30,8292
Non-polymers1,7696
Water3,171176
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3155
Polymers15,4141
Non-polymers9014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2833
Polymers15,4141
Non-polymers8682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.756, 66.594, 68.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dehaloperoxidase B


Mass: 15414.462 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 182 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-94N / 2,6-bis(bromanyl)phenol


Mass: 251.903 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4Br2O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfite, sodium cacodylate, MPEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→30.4 Å / Num. obs: 36705 / % possible obs: 91.92 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 22.6
Reflection shellResolution: 1.554→1.594 Å / Num. unique obs: 2538 / CC1/2: 0.868

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ixf

3ixf


Resolution: 1.554→30.4 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.507 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.096
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2057 1785 4.863 %
Rwork0.1459 34920 -
all0.149 --
obs-36705 91.919 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.048 Å2
Baniso -1Baniso -2Baniso -3
1--3.913 Å2-0 Å2-0 Å2
2--1.75 Å2-0 Å2
3---2.164 Å2
Refinement stepCycle: LAST / Resolution: 1.554→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 111 176 2410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132784
X-RAY DIFFRACTIONr_bond_other_d0.0030.0182474
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.6993855
X-RAY DIFFRACTIONr_angle_other_deg1.6241.6235743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6965382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06323.377151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12715478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0771516
X-RAY DIFFRACTIONr_chiral_restr0.1090.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023483
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02713
X-RAY DIFFRACTIONr_nbd_refined0.2910.2790
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.22192
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21323
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1350.218
X-RAY DIFFRACTIONr_nbd_other0.2170.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.223
X-RAY DIFFRACTIONr_mcbond_it3.9211.9441340
X-RAY DIFFRACTIONr_mcbond_other3.9061.9431339
X-RAY DIFFRACTIONr_mcangle_it4.6742.941738
X-RAY DIFFRACTIONr_mcangle_other4.6722.9411739
X-RAY DIFFRACTIONr_scbond_it6.5672.3641444
X-RAY DIFFRACTIONr_scbond_other6.5752.3631437
X-RAY DIFFRACTIONr_scangle_it7.5213.4322095
X-RAY DIFFRACTIONr_scangle_other7.5343.4212082
X-RAY DIFFRACTIONr_lrange_it7.29625.1573471
X-RAY DIFFRACTIONr_lrange_other7.26925.0113447
X-RAY DIFFRACTIONr_rigid_bond_restr7.73635258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.554-1.5940.3241170.2032538X-RAY DIFFRACTION91.3627
1.594-1.6380.31270.1952598X-RAY DIFFRACTION96.6312
1.638-1.6850.2561190.1772539X-RAY DIFFRACTION96.2346
1.685-1.7370.2441290.1532440X-RAY DIFFRACTION95.8582
1.737-1.7940.2421360.1462371X-RAY DIFFRACTION95.7967
1.794-1.8570.2331280.1342272X-RAY DIFFRACTION95.1626
1.857-1.9270.2441070.1332146X-RAY DIFFRACTION92.4497
1.927-2.0060.21180.1231826X-RAY DIFFRACTION83.541
2.006-2.0950.211020.1221852X-RAY DIFFRACTION86.4219
2.095-2.1970.193870.1251961X-RAY DIFFRACTION94.1176
2.197-2.3150.187830.1161844X-RAY DIFFRACTION94.3221
2.315-2.4550.188860.1181768X-RAY DIFFRACTION94.0639
2.455-2.6240.1971070.1251603X-RAY DIFFRACTION93.0359
2.624-2.8340.189710.1311514X-RAY DIFFRACTION91.9907
2.834-3.1030.226790.1461368X-RAY DIFFRACTION90.721
3.103-3.4680.185660.1511223X-RAY DIFFRACTION89.3278
3.468-40.099230.12939X-RAY DIFFRACTION74.4006
4-4.8910.149580.144937X-RAY DIFFRACTION89.8014
4.891-6.8810.288230.229751X-RAY DIFFRACTION88.0546
6.881-30.40.261190.256430X-RAY DIFFRACTION84.5574

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