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- PDB-1lt1: SLIDING HELIX INDUCED CHANGE OF COORDINATION GEOMETRY IN A MODEL ... -

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Basic information

Entry
Database: PDB / ID: 1lt1
TitleSLIDING HELIX INDUCED CHANGE OF COORDINATION GEOMETRY IN A MODEL DI-MN(II) PROTEIN
ComponentsL13G-DF1
KeywordsDE NOVO PROTEIN / ALPHA-HELICAL BUNDLE / PROTEIN DESIGN / SLIDING HELIX
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsDi Costanzo, L. / Geremia, S.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2003
Title: Sliding helix and change of coordination geometry in a model di-MnII protein
Authors: Degrado, W.F. / Di Costanzo, L. / Geremia, S. / Lombardi, A. / Pavone, V. / Randaccio, L.
#1: Journal: J.Am.Chem.Soc. / Year: 2001
Title: Toward the De Novo Design of a Catalytically Active Helix-Bundle: A Substrate-accessible Carboxylate-Bridged Dinuclear Metal Center
Authors: Di Costanzo, L. / Wade, H. / Geremia, S. / Randaccio, L. / Pavone, V. / Degrado, W.F. / Lombardi, A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Inaugural article: Retrostructural Analysis of Metalloproteins: Application to the Design of a Minimal Model for Diiron Proteins
Authors: Lombardi, A. / Summa, C.M. / Geremia, S. / Randaccio, L. / Pavone, V. / Degrado, W.F.
History
DepositionMay 20, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_conn_type / 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_auth_seq_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.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 1.4Nov 20, 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: L13G-DF1
B: L13G-DF1
C: L13G-DF1
D: L13G-DF1
E: L13G-DF1
F: L13G-DF1
G: L13G-DF1
H: L13G-DF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,17820
Polymers46,5188
Non-polymers65912
Water5,224290
1
A: L13G-DF1
B: L13G-DF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8496
Polymers11,6302
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-38 kcal/mol
Surface area6410 Å2
MethodPISA
2
C: L13G-DF1
D: L13G-DF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8496
Polymers11,6302
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-36 kcal/mol
Surface area6430 Å2
MethodPISA
3
E: L13G-DF1
F: L13G-DF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7394
Polymers11,6302
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-32 kcal/mol
Surface area6270 Å2
MethodPISA
4
G: L13G-DF1
H: L13G-DF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7394
Polymers11,6302
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-32 kcal/mol
Surface area6340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.225, 89.270, 146.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
L13G-DF1


Mass: 5814.788 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: This peptide was chemically synthetized.
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.38 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, MANGANESE ACETATE, BUFFER TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
234 %PEG4001reservoir
30.03 M1reservoirMn(CH3COO)2
40.1 MTris-HCl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.91→6.03 Å / Num. all: 38634 / Num. obs: 38634 / % possible obs: 96.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 6.9
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5184 / Rsym value: 0.463 / % possible all: 96.6
Reflection
*PLUS
Num. measured all: 94932

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AB DIMER FROM THE STRUCTURE 1JM0

1jm0


Resolution: 1.91→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24451 1936 5 %RANDOM
Rwork0.20145 ---
obs0.20367 36674 95.5 %-
Displacement parametersBiso mean: 21.179 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2--0.32 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.91→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 12 290 3599
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.030.023
X-RAY DIFFRACTIONp_angle_d2.22
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.22

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