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- PDB-2ygi: Methanobactin HM1 -

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Basic information

Entry
Database: PDB / ID: 2ygi
TitleMethanobactin HM1
ComponentsMETHANOBACTIN HM1
KeywordsMETAL TRANSPORT / METHANOTROPHS
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciesMETHYLOCYSTIS HIRSUTA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.8 Å
AuthorsGhazouani, A. / Basle, A. / Firbank, S.J. / Gray, J. / Dennison, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Variations in Methanobactin Structure Influences Copper Utilization by Methane-Oxidizing Bacteria.
Authors: El Ghazouani, A. / Basle, A. / Gray, J. / Graham, D.W. / Firbank, S.J. / Dennison, C.
History
DepositionApr 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Dec 14, 2016Group: Data collection
Revision 1.4May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_rmsd_angle / struct_conn / struct_conn_type / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METHANOBACTIN HM1
B: METHANOBACTIN HM1
C: METHANOBACTIN HM1
D: METHANOBACTIN HM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5628
Polymers3,3084
Non-polymers2544
Water45025
1
A: METHANOBACTIN HM1
hetero molecules


  • defined by author&software
  • 890 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)8902
Polymers8271
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: METHANOBACTIN HM1
hetero molecules


  • defined by author&software
  • 890 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)8902
Polymers8271
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: METHANOBACTIN HM1
hetero molecules


  • defined by author&software
  • 890 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)8902
Polymers8271
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: METHANOBACTIN HM1
hetero molecules


  • defined by author&software
  • 890 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)8902
Polymers8271
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)9.072, 22.535, 23.572
Angle α, β, γ (deg.)64.79, 86.06, 91.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
METHANOBACTIN HM1


Mass: 826.897 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) METHYLOCYSTIS HIRSUTA (bacteria) / Strain: CSC1
#2: Chemical
ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.02 % / Description: NONE
Crystal growpH: 5.6
Details: 3.8 AMMONIUM SULFATE, 100 MM SODIUM CITRATE PH 5.6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.8
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.8→19.44 Å / Num. obs: 12760 / % possible obs: 75.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 0.8→0.84 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.3 / % possible all: 20.2

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: NONE

Resolution: 0.8→30 Å / Num. parameters: 2267 / Num. restraintsaints: 1929 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.0894 685 5 %RANDOM
all0.0763 13445 --
obs0.0652 -75.8 %-
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 117.76 / Occupancy sum non hydrogen: 241
Refinement stepCycle: LAST / Resolution: 0.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms212 0 4 25 241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.02
X-RAY DIFFRACTIONs_approx_iso_adps0

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