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- PDB-4kmv: Structure of the L100F MUTANT OF DEHALOPEROXIDASE-HEMOGLOBIN A FR... -

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Basic information

Entry
Database: PDB / ID: 4kmv
TitleStructure of the L100F MUTANT OF DEHALOPEROXIDASE-HEMOGLOBIN A 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 / OXYGEN MOLECULE / 2,4,6-trichlorophenol / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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_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

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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)32,94410
Polymers31,1652
Non-polymers1,7798
Water7,296405
1
A: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4915
Polymers15,5831
Non-polymers9084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4535
Polymers15,5831
Non-polymers8714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.539, 67.804, 68.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 15582.612 Da / Num. of mol.: 2 / Mutation: L100F
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

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Non-polymers , 6 types, 413 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-T6C / 2,4,6-trichlorophenol / 2,4,6-Trichlorophenol


Mass: 197.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H3Cl3O
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
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-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. all: 50290 / Num. obs: 49456 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.054 / Χ2: 1.89 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.44-1.4630.5417901.056172
1.46-1.494.40.51624011.135197
1.49-1.525.40.46724481.133198.7
1.52-1.555.90.41124741.23199.9
1.55-1.586.50.36424801.2441100
1.58-1.6270.30524661.2361100
1.62-1.667.20.25725171.3191100
1.66-1.717.30.22124651.3451100
1.71-1.767.30.18324951.5091100
1.76-1.817.30.15324781.6241100
1.81-1.887.30.13525151.851100
1.88-1.957.20.11924952.2051100
1.95-2.047.30.09325002.2951100
2.04-2.157.20.07825072.5041100
2.15-2.297.30.06325202.3521100
2.29-2.467.30.05625152.3441100
2.46-2.717.20.05225422.6471100
2.71-3.17.20.04425732.6091100
3.1-3.917.20.03625782.3991100
3.91-506.60.03526972.232199

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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: 1.44→37.21 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.2077 / WRfactor Rwork: 0.1349 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8795 / SU B: 2.692 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0718 / SU Rfree: 0.0731 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 2502 5.1 %RANDOM
Rwork0.1331 ---
all0.204 49937 --
obs0.1364 49386 98.9 %-
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: 95.38 Å2 / Biso mean: 24.6427 Å2 / Biso min: 6.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0 Å2
2---0.37 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.44→37.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 116 405 2707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192525
X-RAY DIFFRACTIONr_bond_other_d0.0010.022335
X-RAY DIFFRACTIONr_angle_refined_deg1.9162.0053450
X-RAY DIFFRACTIONr_angle_other_deg1.03335390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9315320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65523.952124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94415450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0531517
X-RAY DIFFRACTIONr_chiral_restr0.1710.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022947
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02654
X-RAY DIFFRACTIONr_mcbond_it3.4941.9651147
X-RAY DIFFRACTIONr_mcbond_other3.4911.9651146
X-RAY DIFFRACTIONr_mcangle_it42.9721444
X-RAY DIFFRACTIONr_rigid_bond_restr5.07234860
X-RAY DIFFRACTIONr_sphericity_free38.825596
X-RAY DIFFRACTIONr_sphericity_bonded15.14955092
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 147 -
Rwork0.259 3014 -
all-3161 -
obs--87.18 %

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