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- PDB-3agt: Hemerythrin-like domain of DcrH (met) -

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Basic information

Entry
Database: PDB / ID: 3agt
TitleHemerythrin-like domain of DcrH (met)
ComponentsHemerythrin-like domain protein DcrH
KeywordsMETAL BINDING PROTEIN / OXYGEN BINDING / DIIRON / FOUR-HELIX BUNDLE
Function / homology
Function and homology information


lysozyme activity / 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: 1.4 Å
AuthorsOnoda, A. / Okamoto, Y. / Sugimoto, H. / Mizohata, E. / Inoue, T. / Shiro, Y. / Hayashi, T.
CitationJournal: to be published
Title: Characteristics of Diiron Site with Large Cavity in Hemerythrin-like Domain of DcrH
Authors: Onoda, A. / Okamoto, Y. / Sugimoto, H. / Mizohata, E. / Inoue, T. / Shiro, Y. / Hayashi, T.
History
DepositionApr 6, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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_ncs_dom_lim / 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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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)32,6434
Polymers32,3172
Non-polymers3262
Water4,936274
1
A: Hemerythrin-like domain protein DcrH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3212
Polymers16,1581
Non-polymers1631
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)16,3212
Polymers16,1581
Non-polymers1631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.311, 44.873, 48.127
Angle α, β, γ (deg.)95.270, 104.200, 90.030
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASPASP3AA14 - 10014 - 100
21ALAALAASPASP3BB14 - 10014 - 100
12VALVALARGARG4AA112 - 133112 - 133
22VALVALARGARG4BB112 - 133112 - 133

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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) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 42.75 % / Mosaicity: 0.224 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24 % (W/V) PEG 4000, 0.2M CaCl2, 12 % (V/V) isopropanol, 0.1M TrisHCl, pH 8.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.84 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 1, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 51015 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 10.842 Å2 / Rmerge(I) obs: 0.064 / Χ2: 0.925 / Net I/σ(I): 18.842
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4748 / Χ2: 0.619 / % possible all: 89.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0072refinement
PDB_EXTRACT3.1data extraction
SPACEdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AWY

2awy


Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.199 / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 2549 4.997 %RANDOM
Rwork0.2027 ---
obs-51013 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 8.233 Å2
Baniso -1Baniso -2Baniso -3
1--0.508 Å20.045 Å20.001 Å2
2--0.154 Å20.1 Å2
3---0.372 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 8 274 2528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222446
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9483317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8875297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.37621.773141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90815462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9141538
X-RAY DIFFRACTIONr_chiral_restr0.0960.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021910
X-RAY DIFFRACTIONr_mcbond_it0.7811.51389
X-RAY DIFFRACTIONr_mcangle_it1.40222254
X-RAY DIFFRACTIONr_scbond_it2.38331057
X-RAY DIFFRACTIONr_scangle_it3.7154.51046
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
341TIGHT POSITIONAL0.030.05
191MEDIUM POSITIONAL0.140.5
380LOOSE POSITIONAL0.445
341TIGHT THERMAL0.270.5
191MEDIUM THERMAL0.572
380LOOSE THERMAL0.6210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.4360.2951860.2723140387185.921
1.436-1.4750.2751920.2213397380494.348
1.475-1.5180.2661700.1993346370794.848
1.518-1.5640.2241650.1973310358596.932
1.564-1.6150.2391660.1873204349896.341
1.615-1.6720.1911620.1713086338396.009
1.672-1.7340.231370.1793009323697.219
1.734-1.8050.1981600.1742901313697.608
1.805-1.8840.2281220.1942778298897.055
1.884-1.9750.2091460.1912648287997.048
1.975-2.0810.2271370.1972552275697.569
2.081-2.2060.2011320.22393256298.556
2.206-2.3560.2131220.1992278244198.32
2.356-2.5420.2211290.2042112227598.505
2.542-2.780.221920.2041968209598.329
2.78-3.10.2071060.2131762188499.151
3.1-3.5660.247920.2091546165099.273
3.566-4.3330.245580.1931369143899.235
4.333-5.9890.204440.2081050110099.455
5.989-200.373310.30661566397.436
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)
10.6577-0.4988-0.16081.15120.09990.22650.01090.032-0.0376-0.0578-0.01350.06050.02020.0130.00260.04270.0068-0.01140.0078-0.01640.062122.62827.55814.289
20.57120.45070.17531.49070.12910.2316-0.0015-0.03160.02880.0976-0.00420.037-0.01790.00740.00570.0474-0.0051-0.00410.0074-0.01370.06165.9676.65931.877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA15 - 134
2X-RAY DIFFRACTION2ALLB15 - 134

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