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- PDB-2xjh: Structure and Copper-binding Properties of Methanobactins from Me... -

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Basic information

Entry
Database: PDB / ID: 2xjh
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: 0.92 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
Revision 1.2May 9, 2012Group: Other
Revision 1.3Nov 30, 2012Group: Other
Revision 1.4Jul 24, 2013Group: Non-polymer description / Version format compliance
Revision 2.0Jun 27, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_molecule / pdbx_validate_rmsd_bond / software / struct_conn
Item: _software.name
Revision 2.1May 22, 2019Group: Data collection / Derived calculations / Refinement description
Category: refine / struct_conn
Item: _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHANOBACTIN MB-OB3B
B: METHANOBACTIN MB-OB3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5197
Polymers2,3232
Non-polymers1965
Water21612
1
A: METHANOBACTIN MB-OB3B
hetero molecules


  • defined by author&software
  • 1.27 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,2714
Polymers1,1611
Non-polymers1103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: METHANOBACTIN MB-OB3B
hetero molecules


  • defined by author&software
  • 1.25 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,2483
Polymers1,1611
Non-polymers872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.475, 29.475, 29.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

21B-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.: 2 / 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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 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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.41 Å3/Da / Density % sol: 13 %
Description: PREVIOUSLY SOLVED MODEL CCDC BIDLOQ WAS MANUALLY FITTED INTO DENSITY
Crystal growpH: 7.5 / Details: 4M SODIUM FORMATE, 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: 0.92→20.84 Å / Num. obs: 9025 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.1
Reflection shellResolution: 0.92→0.97 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.5 / % possible all: 78.8

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Processing

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

Resolution: 0.92→20 Å / Num. parameters: 1623 / Num. restraintsaints: 1871 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1405 439 5 %THIN SHELL
obs0.1245 -95.7 %-
all-8586 --
Refine analyzeNum. disordered residues: 13 / Occupancy sum hydrogen: 92 / Occupancy sum non hydrogen: 165.46
Refinement stepCycle: LAST / Resolution: 0.92→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms152 0 5 12 169
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.051
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0349
X-RAY DIFFRACTIONs_zero_chiral_vol0.14
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.148
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.045
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0

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