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

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Entry
Database: PDB / ID: 1ovu
TitleCRYSTAL STRUCTURE OF FOUR-HELIX BUNDLE MODEL di-Co(II)-DF1-L13A (form I)
Componentsfour-helix bundle model di-Co(II)-DF1-L13A (form I)
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 / UNCONVENTIONAL METHOD USING THE GROUP-SUBGROUP RELATION / Resolution: 3.1 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: Acta Crystallogr.,Sect.D / Year: 2003
Title: Phasing protein structures using the group-subgroup relation.
Authors: Di Costanzo, L. / Forneris, F. / Geremia, S. / Randaccio, L.
#2: 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.
#3: 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.
#4: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: four-helix bundle model di-Co(II)-DF1-L13A (form I)
B: four-helix bundle model di-Co(II)-DF1-L13A (form I)
C: four-helix bundle model di-Co(II)-DF1-L13A (form I)
D: four-helix bundle model di-Co(II)-DF1-L13A (form I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,72811
Polymers23,3154
Non-polymers4137
Water18010
1
A: four-helix bundle model di-Co(II)-DF1-L13A (form I)
hetero molecules

A: four-helix bundle model di-Co(II)-DF1-L13A (form I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8936
Polymers11,6582
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2410 Å2
ΔGint-53 kcal/mol
Surface area6410 Å2
MethodPISA
2
B: four-helix bundle model di-Co(II)-DF1-L13A (form I)
hetero molecules

B: four-helix bundle model di-Co(II)-DF1-L13A (form I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7754
Polymers11,6582
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area2600 Å2
ΔGint-45 kcal/mol
Surface area6330 Å2
MethodPISA
3
C: four-helix bundle model di-Co(II)-DF1-L13A (form I)
D: four-helix bundle model di-Co(II)-DF1-L13A (form I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8936
Polymers11,6582
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-57 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.78, 147.72, 37.60
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASP / End label comp-ID: GLY / Refine code: 6 / Auth seq-ID: 1 - 48 / Label seq-ID: 1 - 48

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein/peptide
four-helix bundle model di-Co(II)-DF1-L13A (form I) / di-Co(II)-DF1-L13A (form I)


Mass: 5828.813 Da / Num. of mol.: 4 / 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.: 10 / 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: 2.57 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: CO(CH3COO)2 30 mM, buffer tris 100 mM pH 7.5, peg 400 43%, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50

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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 1, 2001 / 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: 3.1→43.2 Å / Num. obs: 4679 / % possible obs: 97.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.236 / Rsym value: 0.236 / Net I/σ(I): 5.9
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.515 / % possible all: 97.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: UNCONVENTIONAL METHOD USING THE GROUP-SUBGROUP RELATION
Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.843 / SU B: 28.119 / SU ML: 0.511 / Cross valid method: THROUGHOUT / ESU R Free: 0.593
RfactorNum. reflection% reflectionSelection details
Rfree0.30439 220 4.7 %RANDOM
Rwork0.24674 ---
obs0.2496 4679 97.21 %-
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: 58.981 Å2
Baniso -1Baniso -2Baniso -3
1--3.12 Å20 Å20 Å2
2--0.32 Å20 Å2
3---2.8 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 7 10 1669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221700
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8762.0342272
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4663188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.2415358
X-RAY DIFFRACTIONr_chiral_restr0.1860.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021192
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3550.3944
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.591
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3490.3115
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3720.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.0951.5972
X-RAY DIFFRACTIONr_mcangle_it4.07821564
X-RAY DIFFRACTIONr_scbond_it6.9743724
X-RAY DIFFRACTIONr_scangle_it11.24.5696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 414 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.675
2Bloose positional0.765
3Cloose positional0.715
4Dloose positional0.845
1Aloose thermal11.0210
2Bloose thermal7.8710
3Cloose thermal7.8610
4Dloose thermal10.810
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.406 16
Rwork0.285 306

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