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- PDB-3kun: X-ray structure of the metcyano form of dehaloperoxidase from amp... -

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Basic information

Entry
Database: PDB / ID: 3kun
TitleX-ray structure of the metcyano form of dehaloperoxidase from amphitrite ornata: evidence for photoreductive lysis of iron-cyanide bond
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / Crystal structure of metcyano form of dehaloperoxydase / heme / oxygen transport / peroxidase / transport / transport protein
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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsSerrano, V.S. / Chen, Z. / Gaff, J.F. / Rose, R. / Franzen, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: evidence for photoreductive dissociation of the iron-cyanide bond.
Authors: de Serrano, V.S. / Davis, M.F. / Gaff, J.F. / Zhang, Q. / Chen, Z. / D'Antonio, E.L. / Bowden, E.F. / Rose, R. / Franzen, S.
History
DepositionNov 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 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 / 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_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_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)32,5748
Polymers31,0972
Non-polymers1,4776
Water7,134396
1
A: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2874
Polymers15,5491
Non-polymers7393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2874
Polymers15,5491
Non-polymers7393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.252, 66.550, 68.713
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): BL21(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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#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.: 396 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.2 M AMMONIUM SULFATE, 28% 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: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→35 Å / Num. all: 70910 / Num. obs: 67355 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 11.94 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 218.6
Reflection shellResolution: 1.26→1.29 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4989 / Rsym value: 0.324 / % possible all: 95.6

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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 1EW6

1ew6


Resolution: 1.26→35 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.483 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.06 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 3555 5 %RANDOM
Rwork0.153 ---
obs0.155 67355 99.1 %-
all-70910 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.26→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 100 396 2678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223204
X-RAY DIFFRACTIONr_angle_refined_deg1.0262.0384492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1125447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16523.913184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5415620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3141525
X-RAY DIFFRACTIONr_chiral_restr0.0860.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022660
X-RAY DIFFRACTIONr_nbd_refined0.20.21582
X-RAY DIFFRACTIONr_nbtor_refined0.310.22184
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.2123
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.281
X-RAY DIFFRACTIONr_mcbond_it0.7061.51759
X-RAY DIFFRACTIONr_mcangle_it1.1422875
X-RAY DIFFRACTIONr_scbond_it1.64531622
X-RAY DIFFRACTIONr_scangle_it2.2714.51501
LS refinement shellResolution: 1.26→1.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 256 -
Rwork0.199 4733 -
obs--95.57 %

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