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- PDB-3ok5: Structure of the H55D mutant of dehaloperoxidase-hemoglobin A fro... -

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Basic information

Entry
Database: PDB / ID: 3ok5
TitleStructure of the H55D mutant of dehaloperoxidase-hemoglobin A from Amphitriti ornata with 4-Bromophenol inhibitor
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / globin / peroxidase / dehaloperoxidase
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 / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
4-BROMOPHENOL / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsZhao, J. / De Serrano, V.S. / Franzen, S.
CitationJournal: To be Published
Title: Effect of the H55D mutation on the kinetics and structure of dehaloperoxidase-hemoglobin A
Authors: Zhao, J. / De Serrano, V.S. / Franzen, S.
History
DepositionAug 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Derived calculations
Revision 1.2Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,11011
Polymers31,0512
Non-polymers2,0599
Water5,386299
1
B: Dehaloperoxidase A
hetero molecules

A: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,11011
Polymers31,0512
Non-polymers2,0599
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area4860 Å2
ΔGint-108 kcal/mol
Surface area13280 Å2
MethodPISA
2
A: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4114
Polymers15,5261
Non-polymers8863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6997
Polymers15,5261
Non-polymers1,1746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.055, 67.600, 68.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dehaloperoxidase A


Mass: 15525.538 Da / Num. of mol.: 2 / Mutation: H55D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Gene: dhpA / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9NAV8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-BML / 4-BROMOPHENOL


Mass: 173.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5BrO
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonuim Sulfate, 34% w/v PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.91339 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91339 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.92
11-H, L, K20.08
ReflectionResolution: 1.72→48.112 Å / Num. all: 29364 / Num. obs: 27608 / % possible obs: 94.02 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 11.24 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 3.38
Reflection shellResolution: 1.72→1.91 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.38 / Num. unique all: 6936 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QFK

2qfk


Resolution: 1.72→35 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.876 / SU B: 3.015 / SU ML: 0.096 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29738 1367 5 %RANDOM
Rwork0.24113 ---
obs0.24384 27608 94.02 %-
all-29364 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.237 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å20 Å2
2---0.39 Å20 Å2
3---2.96 Å2
Refinement stepCycle: LAST / Resolution: 1.72→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 127 299 2604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222803
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0492.0853881
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1475380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38124.599137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35415545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5481520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022208
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.451.51569
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82322582
X-RAY DIFFRACTIONr_scbond_it1.25831234
X-RAY DIFFRACTIONr_scangle_it1.9414.51235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.763 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.569 48 -
Rwork0.485 1216 -
obs-2132 59.29 %

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