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- PDB-1mey: CRYSTAL STRUCTURE OF A DESIGNED ZINC FINGER PROTEIN BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1mey
TitleCRYSTAL STRUCTURE OF A DESIGNED ZINC FINGER PROTEIN BOUND TO DNA
Components
  • CONSENSUS ZINC FINGER
  • DNA (5'-D(*AP*TP*GP*AP*GP*GP*CP*AP*GP*AP*AP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*TP*TP*CP*TP*GP*CP*CP*TP*(C38)P*A)-3')
KeywordsTRANSFERASE/DNA / ZINC FINGER / PROTEIN-DNA INTERACTION / PROTEIN DESIGN / COMPLEX (ZINC FINGER-DNA) / TRANSFERASE-DNA COMPLEX
Function / homologyClassic Zinc Finger / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsKim, C.A. / Berg, J.M.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: A 2.2 A Resolution Crystal Structure of a Designed Zinc Finger Protein Bound to DNA
Authors: Kim, C.A. / Berg, J.M.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Serine at Position 2 in the DNA Recognition Helix of a Cys2-His2 Zinc Finger Peptide is not, in General, Responsible for Base Recognition
Authors: Kim, C.A. / Berg, J.M.
#2: Journal: Science / Year: 1993
Title: Crystal Structure of a Five-Finger GLI-DNA Complex: New Perspectives on Zinc Fingers
Authors: Pavletich, N.P. / Pabo, C.O.
#3: Journal: Nature / Year: 1993
Title: The Crystal Structure of a Two Zinc-Finger Peptide Reveals an Extension to the Rules for Zinc-Finger/DNA Recognition
Authors: Fairall, L. / Schwabe, J.W. / Chapman, L. / Finch, J.T. / Rhodes, D.
#4: Journal: Science / Year: 1991
Title: Zinc Finger-DNA Recognition: Crystal Structure of a Zif268-DNA Complex at 2.1 A
Authors: Pavletich, N.P. / Pabo, C.O.
History
DepositionSep 27, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*TP*GP*AP*GP*GP*CP*AP*GP*AP*AP*CP*T)-3')
B: DNA (5'-D(*TP*AP*GP*TP*TP*CP*TP*GP*CP*CP*TP*(C38)P*A)-3')
D: DNA (5'-D(*AP*TP*GP*AP*GP*GP*CP*AP*GP*AP*AP*CP*T)-3')
E: DNA (5'-D(*TP*AP*GP*TP*TP*CP*TP*GP*CP*CP*TP*(C38)P*A)-3')
C: CONSENSUS ZINC FINGER
F: CONSENSUS ZINC FINGER
G: CONSENSUS ZINC FINGER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,13716
Polymers46,5787
Non-polymers5599
Water2,378132
1
A: DNA (5'-D(*AP*TP*GP*AP*GP*GP*CP*AP*GP*AP*AP*CP*T)-3')
B: DNA (5'-D(*TP*AP*GP*TP*TP*CP*TP*GP*CP*CP*TP*(C38)P*A)-3')
C: CONSENSUS ZINC FINGER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4126
Polymers18,2163
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: DNA (5'-D(*AP*TP*GP*AP*GP*GP*CP*AP*GP*AP*AP*CP*T)-3')
E: DNA (5'-D(*TP*AP*GP*TP*TP*CP*TP*GP*CP*CP*TP*(C38)P*A)-3')
F: CONSENSUS ZINC FINGER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4126
Polymers18,2163
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: CONSENSUS ZINC FINGER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3144
Polymers10,1471
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.070, 165.530, 46.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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DNA chain , 2 types, 4 molecules ADBE

#1: DNA chain DNA (5'-D(*AP*TP*GP*AP*GP*GP*CP*AP*GP*AP*AP*CP*T)-3')


Mass: 4024.649 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*AP*GP*TP*TP*CP*TP*GP*CP*CP*TP*(C38)P*A)-3')


Mass: 4043.456 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 3 molecules CFG

#3: Protein CONSENSUS ZINC FINGER


Mass: 10147.411 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)

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Non-polymers , 3 types, 141 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE ENTRY CONTAINS TWO COMPLEXES AND ONE UNPAIRED PROTEIN MOLECULE WHICH MAKE UP THE ASYMMETRIC ...THE ENTRY CONTAINS TWO COMPLEXES AND ONE UNPAIRED PROTEIN MOLECULE WHICH MAKE UP THE ASYMMETRIC UNIT. THE FIRST COMPLEX WITH CHAIN IDENTIFIERS A, B AND C ARE BETTER DEFINED SHOWING LESS DISORDER THAN THAT OF THE SECOND COMPLEX IDENTIFIED BY CHAINS D, E AND F. ONLY THE THIRD FINGER DOMAIN OF THE UNPAIRED PROTEIN MOLECULE IS MODELED AS NO DENSITY WAS OBSERVED FOR THE OTHER TWO DOMAINS. NUCLEOSIDE +C B 12,E 12 IS A CYTOSINE WITH AN IODINE ATOM COVALENTLY BOUND TO ATOM C5. THE IODINE IS PRESENTED AS A HETATM AT THE END OF CHAIN *B*, *E" .

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 150011
3BIS-TRIS-PROPANE11
4MGCL211
5NACL11
Crystal grow
*PLUS
Temperature: 20 ℃ / PH range low: 7.8 / PH range high: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mMbis-tris propane1reservoir
210 mM1reservoirMgCl2
380-100 mM1reservoirNaCl
422-24 %PEG15001reservoir
51

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Data collection

Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 23392 / % possible obs: 84 % / Redundancy: 6 % / Rmerge(I) obs: 0.088
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 146523

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Processing

Software
NameClassification
X-PLORrefinement
PROCESSdata reduction
PROCESSdata scaling
RefinementResolution: 2.2→6 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.319 -10 %
Rwork0.224 --
obs0.224 19237 -
Displacement parametersBiso mean: 32.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 1054 11 132 2776
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.77
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.86
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.22 Å
RfactorNum. reflection% reflection
Rfree0.32 -11 %
Rwork0.347 350 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PRODNA-RNA.PARAM
X-RAY DIFFRACTION2TOPHCSDX.PRODNA-RNA.TOP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Num. reflection all: 21015 / σ(F): 3 / Rfactor all: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.86

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