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- PDB-5c39: Crystal structure of a designed Mn binding peptide -

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Basic information

Entry
Database: PDB / ID: 5c39
TitleCrystal structure of a designed Mn binding peptide
ComponentsP0 Manganese cluster peptide
KeywordsDE NOVO PROTEIN / Manganese cofactors / Mn4Ca cluster
Function / homologyImmunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / :
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.751 Å
AuthorsSimmons, C.R. / Olson, T.L. / Allen, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1505874 United States
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Design of dinuclear manganese cofactors for bacterial reaction centers.
Authors: Olson, T.L. / Espiritu, E. / Edwardraja, S. / Simmons, C.R. / Williams, J.C. / Ghirlanda, G. / Allen, J.P.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P0 Manganese cluster peptide
B: P0 Manganese cluster peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6884
Polymers12,5782
Non-polymers1102
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-33 kcal/mol
Surface area6570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.162, 52.465, 52.547
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein P0 Manganese cluster peptide


Mass: 6289.149 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: At 140 uM, dialyzed against 15 mM HEPES + MnCl2, overnight. Concentrated to 100 mM and used hanging drop diffusion against 35% 1,4 dioxane mixed 1:1 in the drop.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→26 Å / Num. obs: 10892 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 16.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.751→26 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 582 5.04 %
Rwork0.1996 --
obs0.2014 10892 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102 Å2 / Biso mean: 42.7676 Å2 / Biso min: 17.52 Å2
Refinement stepCycle: LAST / Resolution: 1.751→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 2 93 977
LS refinement shellResolution: 1.75→1.78 Å / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.244

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