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- PDB-3lb1: Two-site competitive inhibition in dehaloperoxidase-hemoglobin -

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Basic information

Entry
Database: PDB / ID: 3lb1
TitleTwo-site competitive inhibition in dehaloperoxidase-hemoglobin
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / PEROXIDASE / GLOBIN / Heme / Oxygen transport / Transport
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 / 4-IODOPHENOL / Dehaloperoxidase A
Similarity search - Component
Biological speciesAMPHITRITE ORNATA (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
Authorsde Serrano, V.S. / Franzen, S. / Thompson, M.K. / Davis, M.F. / Niccoletti, F.P. / Howes, B.D. / Smulevich, G.
CitationJournal: Biophys.J. / Year: 2010
Title: Internal binding of halogenated phenols in dehaloperoxidase-hemoglobin inhibits peroxidase function.
Authors: Thompson, M.K. / Davis, M.F. / de Serrano, V. / Nicoletti, F.P. / Howes, B.D. / Smulevich, G. / Franzen, S.
History
DepositionJan 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)32,9628
Polymers31,0972
Non-polymers1,8656
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-75 kcal/mol
Surface area13100 Å2
MethodPISA
2
A: Dehaloperoxidase A
hetero molecules

B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9628
Polymers31,0972
Non-polymers1,8656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_544x+1/2,-y-1/2,-z-11
Buried area4270 Å2
ΔGint-74 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.838, 67.254, 69.128
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: 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
#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-IOL / 4-IODOPHENOL


Mass: 220.008 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5IO
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 43.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.2 M AMMONIUM SULFATE, 32% 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-ID / Wavelength: 1.5 / Wavelength: 1.5 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.76→35 Å / Num. all: 25737 / Num. obs: 24442 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 37.94
Reflection shellResolution: 1.76→1.81 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 13.15 / Num. unique all: 1737 / % possible all: 87.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QFK

2qfk


Resolution: 1.76→35 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 2.889 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.169 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1295 5 %RANDOM
Rwork0.186 ---
obs0.188 24442 94.2 %-
all-25737 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.76→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 112 268 2562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222911
X-RAY DIFFRACTIONr_angle_refined_deg1.1242.054054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0945407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95924.14157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69115569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2471526
X-RAY DIFFRACTIONr_chiral_restr0.0790.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022352
X-RAY DIFFRACTIONr_nbd_refined0.1970.21440
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21978
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.238
X-RAY DIFFRACTIONr_mcbond_it0.4221.51643
X-RAY DIFFRACTIONr_mcangle_it0.73322705
X-RAY DIFFRACTIONr_scbond_it1.22431385
X-RAY DIFFRACTIONr_scangle_it1.8394.51266
LS refinement shellResolution: 1.76→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 83 -
Rwork0.246 1654 -
obs-1654 87.82 %

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