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Basic information

Entry
Database: PDB / ID: 2xji
TitleStructure and Copper-binding Properties of Methanobactins from Methylosinus trichosporium OB3b
ComponentsMETHANOBACTIN MB-OB3B
KeywordsOXIDOREDUCTASE / METAL TRANSPORT / METHANOTROPHS / OXAZALONE
Function / homology
Function and homology information


copper ion transport / superoxide dismutase / superoxide dismutase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / extracellular region / metal ion binding / cytoplasm
Similarity search - Function
Methanobactin precursor, Mb-OB3b
Similarity search - Domain/homology
METHANOBACTIN / COPPER (II) ION / Methanobactin mb-OB3b
Similarity search - Component
Biological speciesMETHYLOSINUS TRICHOSPORIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1 Å
AuthorsEl-Ghazouani, A. / Basle, A. / Firbank, S.J. / Knapp, C.W. / Gray, J. / Graham, D.W. / Dennison, C.
Citation
Journal: Inorg.Chem. / Year: 2011
Title: Copper-Binding Properties and Structures of Methanobactins from Methylosinus Trichosporium Ob3B.
Authors: El Ghazouani, A. / Basle, A. / Firbank, S.J. / Knapp, C.W. / Gray, J. / Graham, D.W. / Dennison, C.
#1: Journal: Science / Year: 2004
Title: Methanobactin, a Copper-Acquisition Compound from Methane-Oxidizing Bacteria.
Authors: Kim, H.J. / Graham, D.W. / Dispirito, A.A. / Alterman, M.A. / Galeva, N. / Larive, C.K. / Asunskis, D. / Sherwood, P.M.A.
#2: Journal: J.Am.Chem.Soc. / Year: 2008
Title: NMR, Mass Spectrometry and Chemical Evidence Reveal a Different Chemical Structure for Methanobactin that Contains Oxazolone Rings.
Authors: Behling, L.A. / Hartsel, S.C. / Lewis, D.E. / Dispirito, A.A. / Choi, D.W. / Masterson, L.R. / Veglia, G. / Gallagher, W.H.
History
DepositionJul 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 9, 2012Group: Other
Revision 1.3Nov 30, 2012Group: Other
Revision 1.4Jul 24, 2013Group: Non-polymer description
Revision 2.0May 22, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_source / pdbx_database_proc / pdbx_database_status / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_bond / refine / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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: METHANOBACTIN MB-OB3B
B: METHANOBACTIN MB-OB3B
C: METHANOBACTIN MB-OB3B
D: METHANOBACTIN MB-OB3B
E: METHANOBACTIN MB-OB3B
F: METHANOBACTIN MB-OB3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,35012
Polymers6,9686
Non-polymers3816
Water1,22568
1
A: METHANOBACTIN MB-OB3B
hetero molecules


  • defined by author
  • 1.22 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,2252
Polymers1,1611
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: METHANOBACTIN MB-OB3B
hetero molecules


  • defined by author
  • 1.22 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,2252
Polymers1,1611
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: METHANOBACTIN MB-OB3B
hetero molecules


  • defined by author
  • 1.22 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,2252
Polymers1,1611
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: METHANOBACTIN MB-OB3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,2252
Polymers1,1611
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: METHANOBACTIN MB-OB3B
hetero molecules


  • defined by author
  • 1.22 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,2252
Polymers1,1611
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: METHANOBACTIN MB-OB3B
hetero molecules


  • defined by author
  • 1.22 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,2252
Polymers1,1611
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: METHANOBACTIN MB-OB3B
B: METHANOBACTIN MB-OB3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4504
Polymers2,3232
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-16.2 kcal/mol
Surface area1580 Å2
MethodPISA
8
C: METHANOBACTIN MB-OB3B
D: METHANOBACTIN MB-OB3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4504
Polymers2,3232
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-16.1 kcal/mol
Surface area1560 Å2
MethodPISA
9
E: METHANOBACTIN MB-OB3B
F: METHANOBACTIN MB-OB3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4504
Polymers2,3232
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-24.7 kcal/mol
Surface area1430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.710, 39.570, 85.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-2005-

HOH

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Components

#1: Protein/peptide
METHANOBACTIN MB-OB3B / COPPER-BINDING COMPOUND / CBC / HYDROGEN PEROXIDE REDUCTASE / SUPEROXIDE DISMUTASE / MINUS-MET METHANOBACTIN


Type: Chalkophore, Polypeptide / Class: Metal transport / Mass: 1161.373 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: NCIMB 11131 / Source: (natural) METHYLOSINUS TRICHOSPORIUM (bacteria) / Strain: OB3B
References: UniProt: E3YBA4, METHANOBACTIN, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases, superoxide dismutase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Type: Chalkophore, Polypeptide / Class: Metal transport / Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / References: METHANOBACTIN
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMETHANOBACTIN IS A MEMBER OF THE FAMILY OF CHALKOPHORES, A COPPER CHELATING AGENT INVOLVED IN ...METHANOBACTIN IS A MEMBER OF THE FAMILY OF CHALKOPHORES, A COPPER CHELATING AGENT INVOLVED IN SCAVENGING, UPTAKE AND SUPPRESSION OF TOXICITY OF COPPER. GROUP: 1 NAME: METHANOBACTIN CHAIN: A, B, C, D, E, F COMPONENT_1: METHANOBACTIN PEPTIDE, RESIDUES 0 TO 10 COMPONENT_2: COPPER ATOM, RESIDUE 1001 DESCRIPTION: METHANOBACTIN IS A COPPER BINDING COMPOUND HAVING ANTIBIOTIC AND ANTIOXIDANT ACTIVITY ISOLATED FROM METHANOTROPHIC BACTERIA. METHANOBACTIN MAY FUNCTION IN COPPER UPTAKE, REGULATION OF METHANE MONOOXYGENASE EXPRESSION, PROTECTION AGAINST COPPER TOXICITY, AND PARTICULATE METHANE MONOOXYGENASE ACTIVITY. METHANOBACTIN CAN EXTRACT COPPER FROM INSOLUBLE MINERALS AND COULD BE IMPORTANT FOR MINERAL WEATHERING. MANY METHANOBACTIN PROPERTIES ARE REMINISCENT OF IRON SIDEROPHORES SUGGESTING A SIMILAR MECHANISM OF HANDLING. METHANOBACTIN-LIKE COMPOUNDS HAVE ALSO BEEN IDENTIFIED IN YEAST MITOCHONDRIA, SUGGEST THAT THESE MOLECULES ARE A MORE UNIVERSAL PHENOMENON.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.15 %
Description: PREVIOUSLY SOLVED MODEL CCDC BIDLOQ WAS MANUALLY FITTED INTO DENSITY
Crystal growpH: 7.5 / Details: 2M AMMONIUM SULFATE, 5% ISOPROPANOL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1→21.14 Å / Num. obs: 29329 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.5
Reflection shellResolution: 1→1.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 13.5 / % possible all: 100

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Processing

Software
NameClassification
SHELXL-97refinement
iMOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1→20 Å / Num. parameters: 5724 / Num. restraintsaints: 8640 / Cross valid method: FREE R-VALUE / σ(F): 2 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1291 1469 5 %THIN SHELL
obs0.1137 -94.8 %-
all-27860 --
Refine analyzeNum. disordered residues: 35 / Occupancy sum hydrogen: 252 / Occupancy sum non hydrogen: 471
Refinement stepCycle: LAST / Resolution: 1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms408 0 6 68 482
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.026
X-RAY DIFFRACTIONs_angle_d0.062
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0239
X-RAY DIFFRACTIONs_zero_chiral_vol0.104
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.037
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0

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