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

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Basic information

Entry
Database: PDB / ID: 8vkc
TitleCrystal structure of dehaloperoxidase A in complex with substrate 4-nitrophenol
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / peroxidase / peroxigenase / oxidase / oxigenase / globin / heme cofactor / oxigen binding / hydrogen peroxide co-substrate / halphenol 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
PROTOPORPHYRIN IX CONTAINING FE / P-NITROPHENOL / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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

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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)32,98910
Polymers31,0972
Non-polymers1,8918
Water1,856103
1
AAA: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3964
Polymers15,5491
Non-polymers8483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5926
Polymers15,5491
Non-polymers1,0445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.824, 67.936, 68.276
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 , 5 types, 111 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-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
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: Sep 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→30.43 Å / Num. obs: 16983 / % possible obs: 93.05 % / Redundancy: 3.7 % / CC1/2: 0.98 / Net I/σ(I): 12.4
Reflection shellResolution: 2.03→2.083 Å / Num. unique obs: 973 / CC1/2: 0.314

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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: 2.03→30.43 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.901 / SU B: 15.382 / SU ML: 0.183 / Cross valid method: FREE R-VALUE / ESU R Free: 0.233
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2745 841 4.952 %
Rwork0.1541 16142 -
all0.16 --
obs-16983 93.047 %
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: 28.825 Å2
Baniso -1Baniso -2Baniso -3
1--0.758 Å2-0 Å20 Å2
2--0.632 Å2-0 Å2
3---0.127 Å2
Refinement stepCycle: LAST / Resolution: 2.03→30.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 127 103 2412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132576
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152354
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.7053519
X-RAY DIFFRACTIONr_angle_other_deg1.381.6255420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0155322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0921.831142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32415454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4251520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023072
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02680
X-RAY DIFFRACTIONr_nbd_refined0.2130.2677
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22143
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21245
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21058
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2112
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0960.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.223
X-RAY DIFFRACTIONr_nbd_other0.1830.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.216
X-RAY DIFFRACTIONr_mcbond_it3.8252.8151204
X-RAY DIFFRACTIONr_mcbond_other3.8262.8151203
X-RAY DIFFRACTIONr_mcangle_it4.7854.2281536
X-RAY DIFFRACTIONr_mcangle_other4.7844.2291537
X-RAY DIFFRACTIONr_scbond_it4.4943.1531372
X-RAY DIFFRACTIONr_scbond_other4.4583.1411359
X-RAY DIFFRACTIONr_scangle_it5.6284.5891977
X-RAY DIFFRACTIONr_scangle_other5.624.5721959
X-RAY DIFFRACTIONr_lrange_it5.99833.7543188
X-RAY DIFFRACTIONr_lrange_other5.99533.7193183
X-RAY DIFFRACTIONr_rigid_bond_restr2.19334930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.0830.307660.234973X-RAY DIFFRACTION79.2525
2.083-2.140.433470.2061131X-RAY DIFFRACTION89.3101
2.14-2.2020.364430.1831075X-RAY DIFFRACTION90.38
2.202-2.270.372560.1931067X-RAY DIFFRACTION91.3751
2.27-2.3440.287630.1541038X-RAY DIFFRACTION92.8331
2.344-2.4260.274650.136993X-RAY DIFFRACTION92.8885
2.426-2.5170.247470.143975X-RAY DIFFRACTION92.3216
2.517-2.620.291480.133958X-RAY DIFFRACTION93.321
2.62-2.7360.319330.142916X-RAY DIFFRACTION93.4055
2.736-2.8690.318560.14881X-RAY DIFFRACTION94.8381
2.869-3.0230.294420.128852X-RAY DIFFRACTION95.2077
3.023-3.2060.277370.138798X-RAY DIFFRACTION93.0881
3.206-3.4260.279310.14765X-RAY DIFFRACTION94.2012
3.426-3.6990.239390.156725X-RAY DIFFRACTION98.0745
3.699-4.050.223370.142690X-RAY DIFFRACTION99.7257
4.05-4.5240.25510.12633X-RAY DIFFRACTION100
4.524-5.2160.254290.138554X-RAY DIFFRACTION100
5.216-6.370.216180.197494X-RAY DIFFRACTION100
6.37-8.9310.179190.183392X-RAY DIFFRACTION99.5157
8.931-30.430.366140.198232X-RAY DIFFRACTION96.4706

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