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Basic information

Entry
Database: PDB / ID: 2awy
Titlemet-DcrH-Hr
Componentshemerythrin-like domain protein DcrH
KeywordsOXYGEN STORAGE/TRANSPORT / Hemerythrin-like oxygen sensor / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


Hemerythrin-like / Hemerythrin, metal-binding domain / Haemerythrin, iron-binding site / Hemerythrin-like superfamily / Hemerythrin family signature. / Hemerythrin-like / Hemerythrin HHE cation binding domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MU-OXO-DIIRON / Hemerythrin-like domain protein DcrH
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsIsaza, C.E. / Silaghi-Dumitrescu, R. / Iyer, R.B. / Kurtz, D.M. / Chan, M.K.
CitationJournal: Biochemistry / Year: 2006
Title: Structural Basis for O(2) Sensing by the Hemerythrin-like Domain of a Bacterial Chemotaxis Protein: Substrate Tunnel and Fluxional N Terminus
Authors: Isaza, C.E. / Silaghi-Dumitrescu, R. / Iyer, R.B. / Kurtz, D.M. / Chan, M.K.
History
DepositionSep 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_label_atom_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_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_conn.ptnr2_label_seq_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

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)32,6837
Polymers32,3172
Non-polymers3665
Water2,684149
1
A: hemerythrin-like domain protein DcrH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3624
Polymers16,1581
Non-polymers2033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hemerythrin-like domain protein DcrH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3213
Polymers16,1581
Non-polymers1632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.160, 44.846, 47.538
Angle α, β, γ (deg.)92.76, 103.49, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein hemerythrin-like domain protein DcrH


Mass: 16158.282 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Plasmid: pDVHR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9REU3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.146 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, CaCl2, isopropanol, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-211.7403
SYNCHROTRONSSRL BL9-221.24
SYNCHROTRONSSRL BL9-231.737
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 7, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
116 pole wigglerMADMx-ray1
216 pole wigglerMADMx-ray1
316 pole wigglerMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.74031
21.241
31.7371

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2741 8.8 %random
Rwork0.221 ---
all-29886 --
obs-28546 92 %-
Solvent computationBsol: 48.936 Å2
Displacement parametersBiso mean: 35.234 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å24.95 Å20.324 Å2
2--13.459 Å23.864 Å2
3----11.84 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 9 149 2404
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2ion3_swap.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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