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- PDB-2qfn: X-ray Crystal Structure Analysis of the Binding Site in the Ferri... -

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Basic information

Entry
Database: PDB / ID: 2qfn
TitleX-ray Crystal Structure Analysis of the Binding Site in the Ferric and Oxyferrous Forms of the Recombinant Heme Dehaloperoxidase Cloned from Amphitrite ornata
ComponentsDehaloperoxidase A
KeywordsTRANSPORT PROTEIN / Dehaloperoxidase / DHP / globin / heme protein
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-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / AMMONIUM ION / OXYGEN MOLECULE / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
Authorsde Serrano, V. / Chen, Z. / Davis, M.F. / Franzen, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: X-ray crystal structural analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from Amphitrite ornata
Authors: de Serrano, V. / Chen, Z. / Davis, M.F. / Franzen, S.
History
DepositionJun 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,94911
Polymers31,3272
Non-polymers1,6219
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-82.6 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.938, 67.091, 68.402
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 A


Mass: 15663.727 Da / Num. of mol.: 2 / Mutation: C73S
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)pLysS / References: UniProt: Q9NAV8

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Non-polymers , 5 types, 301 molecules

#2: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 26-32% PEG 4000, 0.2M ammonium sulfate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: Osmic optics
RadiationMonochromator: OSMIC CONFOCAL BLUE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.62→35 Å / Num. obs: 34478 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.058 / Χ2: 1.432 / Net I/σ(I): 14.8
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.553 / Num. unique all: 3388 / Χ2: 1.129 / % possible all: 99.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å14.74 Å
Translation3 Å14.74 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.416 / SU ML: 0.07 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.173 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1738 5 %RANDOM
Rwork0.17 ---
all0.173 34585 --
obs0.173 34429 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.372 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.62→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 107 292 2813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222611
X-RAY DIFFRACTIONr_angle_refined_deg1.1622.0583596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3115352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04524.493138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53815487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2951520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022064
X-RAY DIFFRACTIONr_nbd_refined0.2040.21281
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21800
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.2113
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.247
X-RAY DIFFRACTIONr_mcbond_it1.0551.51529
X-RAY DIFFRACTIONr_mcangle_it1.61822425
X-RAY DIFFRACTIONr_scbond_it2.64731220
X-RAY DIFFRACTIONr_scangle_it3.7334.51124
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 133 -
Rwork0.318 2289 -
obs-2422 96.49 %

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