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- PDB-8vkd: Crystal structure of dehaloperoxidase A in complex with substrate... -

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Basic information

Entry
Database: PDB / ID: 8vkd
TitleCrystal structure of dehaloperoxidase A in complex with substrate 4-nitrocatechol
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / peroxidase / peroxigenase / oxidase / oxigenase / globin / heme cofactor / oxygen binding / hydrogenase co-substrate / halophenol substrates
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-like superfamily
Similarity search - Domain/homology
4-NITROCATECHOL / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAktar, M.S. / de Serrano, V.S. / Ghiladi, R.A. / Franzen, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Biochemistry / Year: 2024
Title: Structural Comparison of Substrate Binding Sites in Dehaloperoxidase A and B.
Authors: Aktar, M.S. / de Serrano, V. / Ghiladi, R.A. / Franzen, S.
History
DepositionJan 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 25, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Dehaloperoxidase A
BBB: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,40314
Polymers31,0972
Non-polymers2,30612
Water3,639202
1
AAA: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8919
Polymers15,5491
Non-polymers1,3428
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5125
Polymers15,5491
Non-polymers9644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.359, 68.036, 68.312
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 AAABBB

#1: Protein Dehaloperoxidase A


Mass: 15548.597 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NAV8

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Non-polymers , 7 types, 214 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-4NC / 4-NITROCATECHOL


Mass: 155.108 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO4
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: MPEG 2000, ammonium sulfate, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→44.411 Å / Num. obs: 51376 / % possible obs: 94.65 % / Redundancy: 4.2 % / CC1/2: 1 / Net I/σ(I): 27.5
Reflection shellResolution: 1.4→1.436 Å / Num. unique obs: 2425 / CC1/2: 0.873

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QFK

2qfk


Resolution: 1.4→44.411 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.319 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.089 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2008 2581 5.024 %
Rwork0.1658 48795 -
all0.168 --
obs-51376 94.65 %
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: 15.537 Å2
Baniso -1Baniso -2Baniso -3
1--2.185 Å2-0 Å2-0 Å2
2--0.064 Å2-0 Å2
3---2.121 Å2
Refinement stepCycle: LAST / Resolution: 1.4→44.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 153 202 2538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132867
X-RAY DIFFRACTIONr_bond_other_d0.0040.0152596
X-RAY DIFFRACTIONr_angle_refined_deg1.9981.7023922
X-RAY DIFFRACTIONr_angle_other_deg1.6621.6286009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7155365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39822.469162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67315509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6111521
X-RAY DIFFRACTIONr_chiral_restr0.0990.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023488
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02742
X-RAY DIFFRACTIONr_nbd_refined0.3170.2790
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22270
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21305
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21007
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2169
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1140.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2730.259
X-RAY DIFFRACTIONr_nbd_other0.2710.2154
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2480.232
X-RAY DIFFRACTIONr_mcbond_it2.3561.3321338
X-RAY DIFFRACTIONr_mcbond_other2.3531.3321337
X-RAY DIFFRACTIONr_mcangle_it2.6682.0151736
X-RAY DIFFRACTIONr_mcangle_other2.6682.0151737
X-RAY DIFFRACTIONr_scbond_it3.1391.6741529
X-RAY DIFFRACTIONr_scbond_other3.1421.6681516
X-RAY DIFFRACTIONr_scangle_it3.5682.382183
X-RAY DIFFRACTIONr_scangle_other3.5632.3672165
X-RAY DIFFRACTIONr_lrange_it3.91716.8043561
X-RAY DIFFRACTIONr_lrange_other3.74816.5663523
X-RAY DIFFRACTIONr_rigid_bond_restr8.48435463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4360.3631380.2952425X-RAY DIFFRACTION65.0343
1.436-1.4750.3011690.233046X-RAY DIFFRACTION83.3117
1.475-1.5180.281650.2013228X-RAY DIFFRACTION89.9046
1.518-1.5650.2131650.1973219X-RAY DIFFRACTION93.2231
1.565-1.6160.2041700.1763225X-RAY DIFFRACTION95.7417
1.616-1.6730.2172050.1693194X-RAY DIFFRACTION98.8369
1.673-1.7360.1941540.163163X-RAY DIFFRACTION99.9699
1.736-1.8070.1971460.1513031X-RAY DIFFRACTION99.8429
1.807-1.8870.1741680.152916X-RAY DIFFRACTION99.9676
1.887-1.9790.1771500.1442782X-RAY DIFFRACTION99.8978
1.979-2.0860.1821300.1412686X-RAY DIFFRACTION99.929
2.086-2.2120.1691010.1412541X-RAY DIFFRACTION99.8866
2.212-2.3640.1541620.1332339X-RAY DIFFRACTION99.96
2.364-2.5530.1761110.1382230X-RAY DIFFRACTION99.9573
2.553-2.7960.166950.1482057X-RAY DIFFRACTION99.9536
2.796-3.1250.1981010.1521864X-RAY DIFFRACTION99.9491
3.125-3.6060.196840.1631668X-RAY DIFFRACTION99.7722
3.606-4.410.203980.1611383X-RAY DIFFRACTION99.7978
4.41-6.210.283500.2171139X-RAY DIFFRACTION99.6647
6.21-44.4110.308190.288659X-RAY DIFFRACTION95.2247

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