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- PDB-3whn: Hemerythrin-like domain of DcrH I119H mutant (met) -

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Basic information

Entry
Database: PDB / ID: 3whn
TitleHemerythrin-like domain of DcrH I119H mutant (met)
ComponentsHemerythrin-like domain protein DcrH
KeywordsMETAL BINDING PROTEIN / metal-binding / helix bundle / OXYGEN SENSOR
Function / homology
Function and homology information


signal transduction / membrane / metal ion binding
Similarity search - Function
Hemerythrin-like / Hemerythrin, metal-binding domain / Haemerythrin, iron-binding site / Hemerythrin-like superfamily / Hemerythrin family signature. / Hemerythrin-like / Hemerythrin HHE cation binding domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. ...Hemerythrin-like / Hemerythrin, metal-binding domain / Haemerythrin, iron-binding site / Hemerythrin-like superfamily / Hemerythrin family signature. / Hemerythrin-like / Hemerythrin HHE cation binding domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CHLORO DIIRON-OXO MOIETY / Methyl-accepting chemotaxis protein DcrH / Hemerythrin-like domain protein DcrH
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOkamoto, Y. / Onoda, A. / Sugimoto, H. / Takano, Y. / Hirota, S. / Kurtz Jr., D.M. / Shiro, Y. / Hayashi, T.
CitationJournal: Chem.Commun.(Camb.) / Year: 2014
Title: H2O2-dependent substrate oxidation by an engineered diiron site in a bacterial hemerythrin.
Authors: Okamoto, Y. / Onoda, A. / Sugimoto, H. / Takano, Y. / Hirota, S. / Kurtz Jr., D.M. / Shiro, Y. / Hayashi, T.
History
DepositionAug 29, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemerythrin-like domain protein DcrH
B: Hemerythrin-like domain protein DcrH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7736
Polymers32,3672
Non-polymers4064
Water4,864270
1
A: Hemerythrin-like domain protein DcrH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3863
Polymers16,1831
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hemerythrin-like domain protein DcrH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3863
Polymers16,1831
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.573, 44.082, 46.715
Angle α, β, γ (deg.)92.710, 102.590, 90.020
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hemerythrin-like domain protein DcrH


Mass: 16183.272 Da / Num. of mol.: 2 / Mutation: I119H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Hildenborough / Gene: dcrH / Plasmid: pET-16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9REU3, UniProt: Q726F3*PLUS
#2: Chemical ChemComp-CFO / CHLORO DIIRON-OXO MOIETY


Mass: 163.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: ClFe2O
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 30 % (W/V) PEG 4000, 0.2M CaCl2, 12% (V/V) isopropanol, 0.1M TrisHCl, pH 8.2, vapor diffusion, hanging drop, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 17, 2013 / Details: mirrors
Diffraction measurementDetails: 1.00 degrees, 1.9 sec, detector distance 165.00 mm
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.098 / Number: 79685
ReflectionResolution: 1.9→30 Å / Num. obs: 20052 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 14.282
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4.167 / Rsym value: 0.323 / % possible all: 96.4
Cell measurementReflection used: 79685

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SPACEdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AGT

3agt


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.887 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.974 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1013 5.1 %RANDOM
Rwork0.1933 ---
obs0.1959 20052 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44 Å2 / Biso mean: 12.5531 Å2 / Biso min: 4.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.23 Å20.01 Å2
2---0.82 Å20.01 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 10 270 2530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192429
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9433298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1185295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55122.429140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56315450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7651532
X-RAY DIFFRACTIONr_chiral_restr0.0990.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021900
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 75 -
Rwork0.223 1367 -
all-1442 -
obs--95.24 %

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