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- PDB-1ovv: CRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (... -

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Entry
Database: PDB / ID: 1ovv
TitleCRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
ComponentsFOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
KeywordsDE NOVO PROTEIN / ALPHA-HELICAL BUNDLE / PROTEIN DESIGN
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 / UNCONVENTIANAL METHOD USING THE GROUP-SUBGROUP RELATION / Resolution: 2.9 Å
AuthorsDi Costanzo, L. / Geremia, S.
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography.
Authors: Geremia, S. / Di Costanzo, L. / Randaccio, L. / Engel, D.E. / Lombardi, A. / Nastri, F. / DeGrado, W.F.
#1: Journal: ANGEW.CHEM.INT.ED.ENGL. / Year: 2003
Title: Sliding Helix Induced Change of Coordination Geomet Model Di-Mn(II) Protein
Authors: Degrado, W.F. / Di Costanzo, L. / Geremia, S. / Lombardi, A. / Pavone, V. / Randaccio, L.
#2: Journal: J.Am.Chem.Soc. / Year: 2001
Title: Toward the De Novo Design of a Catalytically Active Helix-Bundle: A Substrate Accessible Carboxylate-Br Dinuclear Metal Center
Authors: Di Costanzo, L. / Wade, H. / Geremia, S. / Randaccio, L. / Pavone, V. / Degrado, W.F. / Lombardi, A.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: 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
DepositionMar 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr2_symmetry / _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: FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
B: FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
C: FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
D: FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
E: FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
F: FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,38513
Polymers34,9736
Non-polymers4137
Water1267
1
A: FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
B: FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7754
Polymers11,6582
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-45 kcal/mol
Surface area5830 Å2
MethodPISA
2
C: FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
D: FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8345
Polymers11,6582
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-49 kcal/mol
Surface area6150 Å2
MethodPISA
3
E: FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
F: FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7754
Polymers11,6582
Non-polymers1182
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-45 kcal/mol
Surface area5850 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.92, 80.05, 96.62
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form II) / di-Co(II)-DF1-L13A (form II)


Mass: 5828.813 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: THIS PROTEIN WAS CHEMICALLY SYNTHESIZED.
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.03 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Peg 400, TRIS-HCl, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 / Date: Sep 30, 2002 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: 1.2 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.21
21.21
ReflectionResolution: 2.9→33.3 Å / Num. obs: 6492 / % possible obs: 96.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 11.2
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.573 / % possible all: 89

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: UNCONVENTIANAL METHOD USING THE GROUP-SUBGROUP RELATION
Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.903 / SU B: 31.395 / SU ML: 0.588 / Cross valid method: THROUGHOUT / ESU R Free: 0.611
RfactorNum. reflection% reflectionSelection details
Rfree0.31979 309 4.8 %RANDOM
Rwork0.26695 ---
obs0.26943 6492 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.24 Å20 Å20 Å2
2---10.3 Å20 Å2
3---13.54 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 7 7 2492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222550
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5022.0343408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5073282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.08615536
X-RAY DIFFRACTIONr_chiral_restr0.1560.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021788
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3540.31667
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.250.5180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3370.384
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3950.55
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.1691.51458
X-RAY DIFFRACTIONr_mcangle_it4.08722346
X-RAY DIFFRACTIONr_scbond_it6.67931086
X-RAY DIFFRACTIONr_scangle_it10.534.51044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded

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