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BMRB: 16797

2KVH

Structure of the three-Cys2His2 domain of mouse testis zinc finger protein

Authors

Chou, C., Lou, Y., Chen, C.

Assembly

mTZD finger2

Entity

1. mTZD finger2 (polymer, Thiol state: all other bound), 27 monomers, 3120.545 Da Detail

EKPFSCSLCP QRSRDFSAMT KHLRTHG

2. ZN (non-polymer), 65.409 Da

Total weight

3185.9539 Da

Max. entity weight

3120.545 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.1 %, Completeness (bb): 98.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.1 % (291 of 316)	94.6 % (159 of 168)	86.9 % (106 of 122)	100.0 % (26 of 26)
Backbone	98.1 % (155 of 158)	100.0 % (53 of 53)	96.2 % (77 of 80)	100.0 % (25 of 25)
Sidechain	88.0 % (162 of 184)	92.2 % (106 of 115)	80.9 % (55 of 68)	100.0 % (1 of 1)
Aromatic	32.1 % (9 of 28)	57.1 % (8 of 14)	7.1 % (1 of 14)
Methyl	100.0 % (14 of 14)	100.0 % (7 of 7)	100.0 % (7 of 7)

1. mTZD finger2

EKPFSCSLCP QRSRDFSAMT KHLRTHG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	mTZD finger2			0.0 ~ 0.0 mM
2	acetic acid	[U-99% 2H]		50 mM
3	sodium chloride	natural abundance		20 mM

Protein Blocks Logo

Calculated from 15 models in PDB: 2KVH, Strand ID: A Detail

Release date

2010-07-26

Citation

Structure and DNA binding characteristics of the three-Cys(2)His(2) domain of mouse testis zinc finger protein
Chou, C., Lou, Y., Tang, T.K., Chen, C.
Proteins (2010), 78, 2202-2212, PubMed 20544958 , DOI 10.1002/prot.22732 , Abstract

Related entities 1. mTZD finger2, : 1 : 7 : 697 entities Detail

Interaction partners 1. mTZD finger2, : 4 interactors Detail

More details for 4 interactors identified by 4 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	mTZD finger2			0.0 ~ 0.0 mM
2	acetic acid	[U-99% 2H]		50 mM
3	sodium chloride	natural abundance		20 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	mTZD finger2			0.0 ~ 0.0 mM
2	acetic acid	[U-99% 2H]		50 mM
3	sodium chloride	natural abundance		20 mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	mTZD finger2			0.0 ~ 0.0 mM
2	acetic acid	[U-99% 2H]		50 mM
3	sodium chloride	natural abundance		20 mM

4 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	mTZD finger2			0.0 ~ 0.0 mM
2	acetic acid	[U-99% 2H]		50 mM
3	sodium chloride	natural abundance		20 mM

5 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	mTZD finger2			0.0 ~ 0.0 mM
2	acetic acid	[U-99% 2H]		50 mM
3	sodium chloride	natural abundance		20 mM

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	mTZD finger2			0.0 ~ 0.0 mM
2	acetic acid	[U-99% 2H]		50 mM
3	sodium chloride	natural abundance		20 mM

7 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	mTZD finger2			0.0 ~ 0.0 mM
2	acetic acid	[U-99% 2H]		50 mM
3	sodium chloride	natural abundance		20 mM

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	mTZD finger2			0.0 ~ 0.0 mM
2	acetic acid	[U-99% 2H]		50 mM
3	sodium chloride	natural abundance		20 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	mTZD finger2			0.0 ~ 0.0 mM
2	acetic acid	[U-99% 2H]		50 mM
3	sodium chloride	natural abundance		20 mM

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	mTZD finger2			0.0 ~ 0.0 mM
2	acetic acid	[U-99% 2H]		50 mM
3	sodium chloride	natural abundance		20 mM

11 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	mTZD finger2			0.0 ~ 0.0 mM
2	acetic acid	[U-99% 2H]		50 mM
3	sodium chloride	natural abundance		20 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16797_2kvh.nef
Input source #2: Coordindates	2kvh.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:34:CYS:SG	A:37:CYS:SG	reduced, CA 60.066, CB 29.527 ppm	reduced, CA 58.14, CB 29.46 ppm	2.846

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:22:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:26:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:9:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:6:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	Distance restraints

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-30-------40--------50-----
EKPFSCSLCPQRSRDFSAMTKHLRTHG
|||||||||||||||||||||||||||
EKPFSCSLCPQRSRDFSAMTKHLRTHG
--------10--------20-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	27	0	0	100.0

Content subtype: combined_16797_2kvh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assignments_zf2	Warning	291		100.0 (chain: A, length: 27)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	226 (1)	noe	100.0 (chain: A, length: 27)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	4 (1)	undefined	14.8 (chain: A, length: 27), 100.0 (chain: B, length: 1)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	4 (1)	hbond	14.8 (chain: A, length: 27)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	22 (22)	.	77.8 (chain: A, length: 27)

Assigned chemical shifts

Saveframe: assignments_zf2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 159
  - ¹³C chemical shifts: 106
  - ¹⁵N chemical shifts: 26
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
- Total number of restraints: 226
- Weight of restraints: 1.0 (226)
- Potential type of restraints: square-well-parabolic (226)
- Range of distance target values: 2.4, 4.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 14.8%
    - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
  - Total number of restraints: 4
  - Weight of restraints: 1.0 (4)
  - Potential type of restraints: square-well-parabolic (4)
  - Range of distance target values: 2.0, 2.3 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 14.8%
    - Total number of restraints: 4
    - Weight of restraints: 1.0 (4)
    - Potential type of restraints: square-well-parabolic (4)
    - Range of distance target values: 2.05, 3.05 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 77.8%
- Total number of restraints: 22
- Total number of restraints per polymer type: 22
- Weight of restraints: 1.0 (22)
- Potential type of restraints: square-well-parabolic (22)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords protein/DNA