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- PDB-3v1d: Crystal structure of de novo designed MID1-cobalt -

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Basic information

Entry
Database: PDB / ID: 3v1d
TitleCrystal structure of de novo designed MID1-cobalt
ComponentsComputational design, MID1-cobalt
KeywordsDE NOVO PROTEIN / METAL BINDING PROTEIN / Helix-turn-helix / Zinc homodimerization
Function / homologyRabenosyn, Rab binding domain / DNA Excision Repair, Uvrb; Chain A / Few Secondary Structures / Irregular / :
Function and homology information
Biological speciesARTIFICIAL GENE (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.239 Å
AuthorsDer, B.S. / Machius, M. / Miley, M.J. / Kuhlman, B.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer.
Authors: Der, B.S. / Machius, M. / Miley, M.J. / Mills, J.L. / Szyperski, T. / Kuhlman, B.
History
DepositionDec 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Sep 13, 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_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.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.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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

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Assembly

Deposited unit
A: Computational design, MID1-cobalt
B: Computational design, MID1-cobalt
C: Computational design, MID1-cobalt
D: Computational design, MID1-cobalt
E: Computational design, MID1-cobalt
F: Computational design, MID1-cobalt
G: Computational design, MID1-cobalt
H: Computational design, MID1-cobalt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,41820
Polymers43,9938
Non-polymers1,42512
Water7,080393
1
A: Computational design, MID1-cobalt
F: Computational design, MID1-cobalt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3545
Polymers10,9982
Non-polymers3563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-37 kcal/mol
Surface area6190 Å2
MethodPISA
2
B: Computational design, MID1-cobalt
C: Computational design, MID1-cobalt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3545
Polymers10,9982
Non-polymers3563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-36 kcal/mol
Surface area6210 Å2
MethodPISA
3
D: Computational design, MID1-cobalt
G: Computational design, MID1-cobalt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3545
Polymers10,9982
Non-polymers3563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-37 kcal/mol
Surface area6110 Å2
MethodPISA
4
E: Computational design, MID1-cobalt
H: Computational design, MID1-cobalt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3545
Polymers10,9982
Non-polymers3563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-38 kcal/mol
Surface area6120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.720, 45.451, 62.112
Angle α, β, γ (deg.)90.04, 90.00, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
Computational design, MID1-cobalt / Computational redesign of the biological sequence.


Mass: 5499.118 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARTIFICIAL GENE (others) / Plasmid: pQE-80L MBP fusion / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 1.78 Å3/Da / Density % sol: 30.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1-2 microliters protein (20 mg/ml, 100 mM ammonium acetate buffer) mixed with 1 microliter crystallization buffer (0.1 M MES pH 6.0, 30% PEG 200, 10% PEG 3000), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9494 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 26, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9494 Å / Relative weight: 1
ReflectionResolution: 1.239→36.668 Å / Num. all: 81186 / Num. obs: 81186 / % possible obs: 94.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 7.8 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.1
Reflection shellResolution: 1.24→1.25 Å / Redundancy: 2 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2 / % possible all: 82.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_927)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YZM

1yzm


Resolution: 1.239→36.668 Å / SU ML: 0.14 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 19.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1941 1136 1.4 %RANDOM
Rwork0.1467 ---
obs0.1474 81041 94.06 %-
all-81041 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.972 Å2 / ksol: 0.462 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4267 Å2-0.0962 Å20.5379 Å2
2--2.8769 Å2-0.1917 Å2
3----1.4502 Å2
Refinement stepCycle: LAST / Resolution: 1.239→36.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3088 0 72 393 3553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123543
X-RAY DIFFRACTIONf_angle_d1.3234784
X-RAY DIFFRACTIONf_dihedral_angle_d16.5261416
X-RAY DIFFRACTIONf_chiral_restr0.065480
X-RAY DIFFRACTIONf_plane_restr0.006651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.239-1.29540.27171450.22729247X-RAY DIFFRACTION88
1.2954-1.36370.20171530.16339778X-RAY DIFFRACTION92
1.3637-1.44910.18491510.13119904X-RAY DIFFRACTION93
1.4491-1.5610.16161180.11349964X-RAY DIFFRACTION94
1.561-1.71810.17441430.102110108X-RAY DIFFRACTION95
1.7181-1.96670.16411360.115310191X-RAY DIFFRACTION96
1.9667-2.47770.16381430.123210331X-RAY DIFFRACTION97
2.4777-36.68360.22521470.185110382X-RAY DIFFRACTION98

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