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- PDB-3agu: Hemerythrin-like domain of DcrH (semimet-R) -

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Basic information

Entry
Database: PDB / ID: 3agu
TitleHemerythrin-like domain of DcrH (semimet-R)
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: 1.805 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
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 1.3Nov 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.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
Water4,648258
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)33.425, 44.903, 48.076
Angle α, β, γ (deg.)95.210, 103.980, 89.950
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAASPASP3AA14 - 10014 - 100
211ALAALAASPASP3BB14 - 10014 - 100
121VALVALARGARG3AA112 - 133112 - 133
221VALVALARGARG3BB112 - 133112 - 133
112CFOCFOCFOCFO4AC201
212CFOCFOCFOCFO4BD201

NCS ensembles :
ID
1
2

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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.: 258 / 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: 2.16 Å3/Da / Density % sol: 42.98 % / Mosaicity: 2.034 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% (W/V) PEG4000, 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: 0.9 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: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 24033 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.067 Å2 / Rmerge(I) obs: 0.072 / Χ2: 0.995 / Net I/σ(I): 16.259
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2362 / Χ2: 0.812 / % possible all: 95.6

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Processing

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

2awy


Resolution: 1.805→20 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.867 / WRfactor Rfree: 0.282 / WRfactor Rwork: 0.241 / ESU R: 0.212 / ESU R Free: 0.184 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2921 1195 4.974 %RANDOM
Rwork0.2471 ---
obs-24026 96.899 %-
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: 12.104 Å2
Baniso -1Baniso -2Baniso -3
1--0.747 Å2-0.128 Å20.131 Å2
2---0.826 Å2-0.135 Å2
3---1.612 Å2
Refinement stepCycle: LAST / Resolution: 1.805→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 8 258 2512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222443
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9493313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2265299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.74121.942139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91915464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9181536
X-RAY DIFFRACTIONr_chiral_restr0.0880.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021900
X-RAY DIFFRACTIONr_mcbond_it0.6581.51389
X-RAY DIFFRACTIONr_mcangle_it1.07922255
X-RAY DIFFRACTIONr_scbond_it1.74231054
X-RAY DIFFRACTIONr_scangle_it2.7744.51041
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1428TIGHT POSITIONAL0.020.05
1483LOOSE POSITIONAL0.085
1428TIGHT THERMAL0.120.5
1483LOOSE THERMAL0.1310
24MEDIUM POSITIONAL0.010.5
24MEDIUM THERMAL0.472
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 (%)
1.805-1.8520.326690.2791577183989.505
1.852-1.9020.312820.2491591174795.764
1.902-1.9570.347840.2581617176996.156
1.957-2.0160.349790.231486163096.012
2.016-2.0820.288760.2261537167396.414
2.082-2.1540.292840.2281408153897.009
2.154-2.2340.274820.2291440156697.19
2.234-2.3240.298690.2521323142597.684
2.324-2.4260.287790.2271297140498.006
2.426-2.5430.249700.2411241134397.617
2.543-2.6780.323580.2481195127598.275
2.678-2.8370.321540.2621143121598.519
2.837-3.0290.314730.2481056114898.345
3.029-3.2650.244510.248982104998.475
3.265-3.5670.333530.25889996298.961
3.567-3.9730.274400.22885691398.138
3.973-4.5570.237310.23673477698.582
4.557-5.510.219240.22964567399.406
5.51-7.5130.407160.33450152099.423
7.513-200.27210.3130333098.182
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)
11.1191-0.5448-0.19311.19610.08810.42150.0130.0177-0.0517-0.1157-0.01740.04160.0333-0.01810.00440.02940.0057-0.00750.0252-0.00120.012422.90127.46914.243
21.10360.74270.33761.71950.16030.45220.0048-0.04030.06520.1406-0.01480.0273-0.0369-0.02540.010.03740.0185-0.00590.0168-0.0050.00816.1586.69331.811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA15 - 134
2X-RAY DIFFRACTION2ALLB15 - 134

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