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Basic information

Entry
Database: PDB / ID: 4ilz
TitleStructural and kinetic study of an internal substrate binding site of dehaloperoxidase-hemoglobin A from Amphitrite ornata
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / peroxidase / globin
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 / ISOPROPYL ALCOHOL / OXYGEN MOLECULE / 2,4,6-TRIBROMOPHENOL / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
Authorsde Serrano, V.S. / Zhao, J. / Zhao, J. / Franzen, S.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and Kinetic Study of an Internal Substrate Binding Site in Dehaloperoxidase-Hemoglobin A from Amphitrite ornata.
Authors: Zhao, J. / de Serrano, V. / Zhao, J. / Le, P. / Franzen, S.
History
DepositionJan 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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)33,49817
Polymers31,0972
Non-polymers2,40115
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,14113
Polymers15,5491
Non-polymers1,59212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3574
Polymers15,5491
Non-polymers8093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.589, 67.184, 68.910
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: 15548.597 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 201 molecules

#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-TBP / 2,4,6-TRIBROMOPHENOL


Mass: 330.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H3Br3O
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.2 M Ammonium Sulfate, 32% w/v PEG 4000, pH 5.9, 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
Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91339 Å / Relative weight: 1
ReflectionResolution: 1.91→48 Å / Num. all: 20247 / Num. obs: 20174 / % possible obs: 99.64 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 2.18
Reflection shellResolution: 1.91→1.959 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1470 / % possible all: 99.29

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QFK

2qfk


Resolution: 1.91→48 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.859 / SU B: 4.041 / SU ML: 0.122 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.065 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28539 1109 5.2 %RANDOM
Rwork0.24022 ---
obs0.24263 20174 99.64 %-
all-20247 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.724 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å2-0 Å2-0 Å2
2--2.45 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.91→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 146 186 2514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193105
X-RAY DIFFRACTIONr_angle_refined_deg1.2724258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8675402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29424.331157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1415572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9071524
X-RAY DIFFRACTIONr_chiral_restr0.1270.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022500
LS refinement shellResolution: 1.91→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 86 -
Rwork0.381 1460 -
obs--99.29 %

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