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- PDB-3dr9: Increased Distal Histidine Conformational Flexibility in the Deox... -

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Basic information

Entry
Database: PDB / ID: 3dr9
TitleIncreased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase from Amphitrite ornata
ComponentsDehaloperoxidase A
KeywordsOXIDOREDUCTASE / deoxy form of dehaloperoxidase / DHP / heme peroxidase / globin-like / globin / heme protein / Heme / Oxygen transport / Peroxidase / 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 domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Dehaloperoxidase A
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.26 Å
AuthorsChen, X. / de Serrano, V.S. / Betts, L. / Franzen, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Distal histidine conformational flexibility in dehaloperoxidase from Amphitrite ornata.
Authors: Chen, Z. / de Serrano, V. / Betts, L. / Franzen, S.
History
DepositionJul 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)32,6187
Polymers31,0972
Non-polymers1,5215
Water5,170287
1
A: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1652
Polymers15,5491
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dehaloperoxidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4535
Polymers15,5491
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.517, 67.194, 69.094
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)pLysS / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 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 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→35 Å / Num. obs: 79486 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.4
Reflection shellResolution: 1.22→1.26 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.513 / % possible all: 92.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å14.84 Å
Translation3 Å14.84 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.861 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19593 3531 5 %RANDOM
Rwork0.17407 ---
obs0.1752 66956 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.637 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2---1.46 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.26→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 105 288 3163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223036
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.212.0474256
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5925435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82424.566173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02815620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6771527
X-RAY DIFFRACTIONr_chiral_restr0.090.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022471
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21449
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22027
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.2115
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7881.51728
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22122810
X-RAY DIFFRACTIONr_scbond_it1.97231456
X-RAY DIFFRACTIONr_scangle_it2.6694.51337
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.26→1.291 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 219 -
Rwork0.247 4671 -
obs--98.25 %

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