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- PDB-3waq: Hemerythrin-like domain of DcrH I119E mutant (met) -

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Basic information

Entry
Database: PDB / ID: 3waq
TitleHemerythrin-like domain of DcrH I119E 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 ...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
MU-OXO-DIIRON / Methyl-accepting chemotaxis protein DcrH / Hemerythrin-like domain protein DcrH
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOkamoto, Y. / Onoda, A. / Sugimoto, H. / Takano, Y. / Hirota, S. / Kurtz Jr., D.M. / Shiro, Y. / Hayashi, T.
CitationJournal: Inorg.Chem. / Year: 2013
Title: Crystal structure, exogenous ligand binding, and redox properties of an engineered diiron active 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
DepositionMay 7, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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_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_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_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: Hemerythrin-like domain protein DcrH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3022
Polymers16,1741
Non-polymers1281
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.965, 50.859, 76.677
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hemerythrin-like domain protein DcrH


Mass: 16174.239 Da / Num. of mol.: 1 / Mutation: I119E
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-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.87 Å3/Da / Density % sol: 34.1 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 7
Details: 50mM MOPS, 50mg/mL protein, pH 7.0, SMALL TUBES, temperature 277K

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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: Oct 8, 2012 / Details: mirrors
Diffraction measurementDetails: 1.00 degrees, 1.8 sec, detector distance 174.547 mm
Method: \w scans
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: 0.061 / Number: 80030
ReflectionResolution: 1.8→20 Å / Num. obs: 23644 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 25.054
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 4.895 / Rsym value: 0.279 / % possible all: 99.3
Cell measurementReflection used: 80030

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AGT

3agt


Resolution: 1.8→19.712 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8027 / SU ML: 0.23 / Cross valid method: THROUGHOUT / Phase error: 26.43 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1066 4.93 %RANDOM
Rwork0.2068 ---
obs0.2095 21644 99.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.69 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 86.55 Å2 / Biso mean: 27.7712 Å2 / Biso min: 10.69 Å2
Baniso -1Baniso -2Baniso -3
1-9.6156 Å20 Å2-0 Å2
2---0.122 Å20 Å2
3----9.4936 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 3 57 1189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151190
X-RAY DIFFRACTIONf_angle_d1.3221629
X-RAY DIFFRACTIONf_chiral_restr0.082169
X-RAY DIFFRACTIONf_plane_restr0.006207
X-RAY DIFFRACTIONf_dihedral_angle_d16.091454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7957-1.87730.31441310.22412464259596
1.8773-1.97620.32351220.22262593271599
1.9762-2.09990.27081410.219725472688100
2.0999-2.26180.24241180.195726332751100
2.2618-2.48910.27581630.189625592722100
2.4891-2.84830.25951450.207826052750100
2.8483-3.5850.23231260.207125762702100
3.585-19.71270.25811200.20712601272199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.98460.00210.03232.6646-1.5083.14890.0451-0.0959-0.04960.2828-0.1205-0.2480.01470.14690.1130.1333-0.01920.00310.1324-0.0130.155211.43285.957821.6186
22.6431-0.2514-0.30283.4183-0.28582.3826-0.06770.03660.14690.48060.10380.3561-0.0173-0.3185-0.04450.14380.01660.05110.10290.00720.17923.716511.810518.6489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:70)A4 - 70
2X-RAY DIFFRACTION2chain 'A' and (resseq 71:201)A71 - 201

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