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- PDB-1tnd: THE 2.2 ANGSTROMS CRYSTAL STRUCTURE OF TRANSDUCIN-ALPHA COMPLEXED... -

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Basic information

Entry
Database: PDB / ID: 1tnd
TitleTHE 2.2 ANGSTROMS CRYSTAL STRUCTURE OF TRANSDUCIN-ALPHA COMPLEXED WITH GTP GAMMA S
ComponentsTRANSDUCIN
KeywordsBINDING PROTEIN(GTP)
Function / homology
Function and homology information


negative regulation of cyclic-nucleotide phosphodiesterase activity / detection of light stimulus involved in visual perception / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / photoreceptor outer segment membrane / G alpha (i) signalling events / acyl binding / response to light stimulus / phototransduction, visible light ...negative regulation of cyclic-nucleotide phosphodiesterase activity / detection of light stimulus involved in visual perception / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / photoreceptor outer segment membrane / G alpha (i) signalling events / acyl binding / response to light stimulus / phototransduction, visible light / phototransduction / photoreceptor inner segment / G protein-coupled receptor binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / photoreceptor disc membrane / GDP binding / heterotrimeric G-protein complex / GTPase activity / protein kinase binding / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Guanine nucleotide-binding protein G(t) subunit alpha-1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsNoel, J.P. / Hamm, H.E. / Sigler, P.B.
CitationJournal: Nature / Year: 1993
Title: The 2.2 A crystal structure of transducin-alpha complexed with GTP gamma S.
Authors: Noel, J.P. / Hamm, H.E. / Sigler, P.B.
History
DepositionMar 31, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 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_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_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_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.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_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_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: TRANSDUCIN
B: TRANSDUCIN
C: TRANSDUCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,93715
Polymers111,4243
Non-polymers2,51312
Water14,880826
1
A: TRANSDUCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9795
Polymers37,1411
Non-polymers8384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRANSDUCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9795
Polymers37,1411
Non-polymers8384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TRANSDUCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9795
Polymers37,1411
Non-polymers8384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.500, 108.300, 79.000
Angle α, β, γ (deg.)90.00, 112.30, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CAC A 353, CAC B 353, AND CAC C 353 MODIFY CYS A 62, CYS B 62, AND CYS C 62, RESPECTIVELY.
2: CAC A 354, CAC B 354, AND CAC C 354 MODIFY CYS A 210, CYS B 210, AND CYS C 210, RESPECTIVELY.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.08186, -0.70316, 0.7063), (0.73473, -0.52141, -0.43394), (0.6734, 0.48342, 0.55932)41.734, 124.459, 4.848
2given(-0.03644, 0.73688, 0.67504), (-0.76721, -0.45348, 0.45361), (0.640369, -0.50136, 0.58186)-92.24599, 89.062, 27.03
DetailsTHERE ARE THREE COMPLEXES OF TRANSDUCIN ALPHA, GTP GAMMA S, AND MG+2 PER ASYMMETRIC UNIT. THE CHAIN IDENTIFIES ARE A, B, AND C. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *C*.

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Components

#1: Protein TRANSDUCIN


Mass: 37141.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P04695
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details*CAC* IS A CACODYLIC ACID GROUP (DERIVED FROM CRYSTALLIZATION BUFFER - DIMETHYLARSINIC ACID) FOR ...*CAC* IS A CACODYLIC ACID GROUP (DERIVED FROM CRYSTALLIZATION BUFFER - DIMETHYLARSINIC ACID) FOR WHICH ONLY COORDINATES OF ARSENIC ATOM ARE GIVEN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal grow
*PLUS
Temperature: -12.5 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-25 mg/mlprotein1drop
2166 mMsodium cacodylate1drop
3223 mM1dropCaCl2
425 mMbeta-mercaptoethanol1drop
520 %(v/v)glycerol1drop
63.33 %(w/v)PEG80001drop
75 %(w/v)PEG80001reservoir
8250 mMsodium cacodylate1reservoir
9350 mM1reservoirCaCl2
1025 mMbeta-mercaptoethanol1reservoir
1130 %(v/v)glycerol1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 12.6 Å / Num. all: 58732 / Num. obs: 53289 / Rmerge(I) obs: 0.039

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.19 -
obs0.19 53289
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7668 0 105 826 8599
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.8
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_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.19 / Rfactor obs: 0.178 / Rfactor Rfree: 0.304
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.8

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