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- PDB-4hsx: Structure of the L100F mutant of dehaloperoxidase-hemoglobin A fr... -

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Basic information

Entry
Database: PDB / ID: 4hsx
TitleStructure of the L100F mutant of dehaloperoxidase-hemoglobin A from Amphitrite ornata with 4-bromophenol
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / Globin / Oxygen Storage / Peroxidase
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / peroxidase activity / 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
4-BROMOPHENOL / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsThompson, M.K. / Plummer, A. / Franzen, S.
CitationJournal: Biochemistry / Year: 2013
Title: Role of polarity of the distal pocket in the control of inhibitor binding in dehaloperoxidase-hemoglobin.
Authors: Plummer, A. / Thompson, M.K. / Franzen, S.
History
DepositionOct 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)33,22111
Polymers31,1652
Non-polymers2,0559
Water7,350408
1
A: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7527
Polymers15,5831
Non-polymers1,1706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4684
Polymers15,5831
Non-polymers8863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.241, 67.441, 69.338
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) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NAV8, peroxidase

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Non-polymers , 5 types, 417 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BML / 4-BROMOPHENOL


Mass: 173.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5BrO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 43.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32% PEG 4000, 0.2M ammonium sulfate , 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: 0.9184 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.079 / Χ2: 1.697 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.12-1.143.10.242100150.851198.7
1.14-1.163.60.229101430.8871100
1.16-1.183.70.207100650.871100
1.18-1.213.70.191101970.8621100
1.21-1.233.70.178101690.8971100
1.23-1.263.70.159101340.9151100
1.26-1.293.70.146101970.9271100
1.29-1.333.70.139101530.9641100
1.33-1.373.80.127101060.9931100
1.37-1.413.80.117101831.0121100
1.41-1.463.80.108101291.1091100
1.46-1.523.80.097101131.1941100
1.52-1.593.80.091101931.3081100
1.59-1.673.80.086101461.5061100
1.67-1.783.80.083101261.7061100
1.78-1.923.90.091101782.4671100
1.92-2.113.90.09101583.5611100
2.11-2.413.90.073101552.9991100
2.41-3.043.90.065101433.3951100
3.04-503.90.062101024.73199.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→48.34 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 0.705 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1503 5259 5 %RANDOM
Rwork0.1256 ---
obs0.1268 105290 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.77 Å2 / Biso mean: 10.8949 Å2 / Biso min: 3.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.16 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.12→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 128 408 2724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.022562
X-RAY DIFFRACTIONr_angle_refined_deg3.5232.0053517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50524.409127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60115447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9171515
X-RAY DIFFRACTIONr_chiral_restr0.1290.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.022015
X-RAY DIFFRACTIONr_rigid_bond_restr9.92132562
X-RAY DIFFRACTIONr_sphericity_free20.087561
X-RAY DIFFRACTIONr_sphericity_bonded7.59852833
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.149 368 -
Rwork0.123 6874 -
all-7242 -
obs--99.21 %

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