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- PDB-4kn3: Structure of the Y34NS91G double mutant of Dehaloperoxidase from ... -

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Basic information

Entry
Database: PDB / ID: 4kn3
TitleStructure of the Y34NS91G double mutant of Dehaloperoxidase from Amphitrite ornata with 2,4,6-trichlorophenol
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / GLOBIN / OXYGEN STORAGE / PEROXIDASE / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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 / 2,4,6-trichlorophenol / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsWang, C. / Lovelace, L. / Lebioda, L.
CitationJournal: Biochemistry / Year: 2013
Title: Complexes of dual-function hemoglobin/dehaloperoxidase with substrate 2,4,6-trichlorophenol are inhibitory and indicate binding of halophenol to compound I.
Authors: Wang, C. / Lovelace, L.L. / Sun, S. / Dawson, J.H. / Lebioda, L.
History
DepositionMay 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 28, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)32,9569
Polymers30,9392
Non-polymers2,0177
Water5,549308
1
A: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4814
Polymers15,4701
Non-polymers1,0113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4765
Polymers15,4701
Non-polymers1,0064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.982, 67.657, 67.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1 - 137 / Label seq-ID: 1 - 137

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Dehaloperoxidase A


Mass: 15469.501 Da / Num. of mol.: 2 / Mutation: Y34N,S91G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Plasmid: pET16 / Production host: Escherichia coli (E. coli) / 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-T6C / 2,4,6-trichlorophenol


Mass: 197.446 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H3Cl3O
#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.: 308 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28-32% PEG4K, .2M ammonium sulfate, .02M sodium cacodylate, 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: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 26494 / Num. obs: 26181 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.04 / Χ2: 1.951 / Net I/σ(I): 20.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.79-1.822.70.12112321.087197.9
1.82-1.852.90.11413311.239199.4
1.85-1.893.10.10912811.218199.1
1.89-1.933.10.09212801.261199.1
1.93-1.973.10.07812851.292199.2
1.97-2.023.10.0713091.352199.2
2.02-2.073.10.06413061.38199.5
2.07-2.123.10.05912921.487199.5
2.12-2.183.10.05513081.551199.6
2.18-2.263.10.04813081.655199.8
2.26-2.343.10.04713061.764199.8
2.34-2.4330.04313311.789199.9
2.43-2.543.10.04213041.922199.7
2.54-2.673.10.0413271.99199.8
2.67-2.843.10.0413222.197199.5
2.84-3.063.10.03913142.567199.6
3.06-3.373.10.04113353.306199.3
3.37-3.863.10.04613284.821198.7
3.86-4.8630.03413562.854198
4.86-5030.02313261.911190.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIserguidata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→44.52 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.892 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 1326 5.1 %RANDOM
Rwork0.1326 ---
all0.204 35271 --
obs0.1366 26147 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 94.51 Å2 / Biso mean: 26.7159 Å2 / Biso min: 10.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0 Å2
2---0.03 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.78→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 126 308 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192321
X-RAY DIFFRACTIONr_bond_other_d0.0060.022105
X-RAY DIFFRACTIONr_angle_refined_deg1.7422.0173151
X-RAY DIFFRACTIONr_angle_other_deg1.18434812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42524.393107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60515385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0171513
X-RAY DIFFRACTIONr_chiral_restr0.1450.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022693
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02586
X-RAY DIFFRACTIONr_mcbond_it4.2192.291094
X-RAY DIFFRACTIONr_mcbond_other4.1972.2881093
X-RAY DIFFRACTIONr_mcangle_it4.5953.4371364
X-RAY DIFFRACTIONr_rigid_bond_restr5.04434426
X-RAY DIFFRACTIONr_sphericity_free30.633575
X-RAY DIFFRACTIONr_sphericity_bonded14.57654609
Refine LS restraints NCS

Ens-ID: 1 / Number: 7531 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.784→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 107 -
Rwork0.14 1735 -
all-1842 -
obs--95.89 %

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