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- PDB-2rsl: REFINEMENT OF GAMMA DELTA RESOLVASE REVEALS A STRIKINGLY FLEXIBLE... -

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Basic information

Entry
Database: PDB / ID: 2rsl
TitleREFINEMENT OF GAMMA DELTA RESOLVASE REVEALS A STRIKINGLY FLEXIBLE MOLECULE
ComponentsGAMMA DELTA-RESOLVASE
KeywordsSITE-SPECIFIC RECOMBINASE
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA binding
Similarity search - Function
Resolvase, N-terminal catalytic domain / Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / Recombinase, conserved site / Site-specific recombinases active site. / : / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily ...Resolvase, N-terminal catalytic domain / Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / Recombinase, conserved site / Site-specific recombinases active site. / : / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain / Homeobox-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transposon gamma-delta resolvase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsRice, P.A. / Steitz, T.A.
Citation
Journal: Structure / Year: 1994
Title: Refinement of gamma delta resolvase reveals a strikingly flexible molecule.
Authors: Rice, P.A. / Steitz, T.A.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1990
Title: The Crystal Structure of the Catalytic Domain of the Site-Specific Recombination Enzyme Gamma Delta Resolvase at 2.7 Angstroms Resolution
Authors: Sanderson, M.R. / Freemont, P.S. / Rice, P.A. / Goldman, A. / Hatfull, G.F. / Grindley, N.D.F. / Steitz, T.A.
#2: Journal: Embo J. / Year: 1993
Title: Protein-Protein Interactions Directing Resolvase Site-Specific Recombination: A Structure-Function Analysis
Authors: Hughes, R.E. / Rice, P.A. / Steitz, T.A. / Grindley, N.D.F.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1990
Title: Cooperativity Mutants of the Gamma Delta Resolvase Identify an Essential Interdimer Interaction
Authors: Hughes, R.E. / Hatfull, G.F. / Rice, P. / Steitz, T.A. / Grindley, N.D.F.
#4: Journal: J.Mol.Biol. / Year: 1989
Title: Preparation of Heavy-Atom Derivatives Using Site-Directed Mutagenesis. Introduction of Cysteine Residues Into Gamma Delta Resolvase
Authors: Hatfull, G.F. / Sanderson, M.R. / Freemont, P.S. / Raccuia, P.R. / Grindley, N.D.F. / Steitz, T.A.
History
DepositionSep 8, 1993Processing site: BNL
SupersessionApr 30, 1994ID: 1RSL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 16, 2015Group: Other
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: GAMMA DELTA-RESOLVASE
B: GAMMA DELTA-RESOLVASE
C: GAMMA DELTA-RESOLVASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8366
Polymers46,5473
Non-polymers2883
Water2,972165
1
A: GAMMA DELTA-RESOLVASE
B: GAMMA DELTA-RESOLVASE
C: GAMMA DELTA-RESOLVASE
hetero molecules

A: GAMMA DELTA-RESOLVASE
B: GAMMA DELTA-RESOLVASE
C: GAMMA DELTA-RESOLVASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,67112
Polymers93,0956
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)76.800, 191.300, 63.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-743-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.72553, 0.07192, -0.68442), (-0.0001, -0.99454, -0.1044), (-0.68819, -0.07568, 0.72157)68.86822, 81.59939, 32.52771
2given(-0.48659, -0.12903, 0.86405), (-0.04274, 0.99136, 0.12397), (-0.87258, 0.02339, -0.48791)16.80315, 52.67612, 73.88525
3given(-0.24741, 0.03908, 0.96812), (0.01498, -0.99891, 0.04415), (0.96879, 0.02542, 0.24656)-0.80348, 131.60529, -2.98717
DetailsTHE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW WERE CALCULATED BY A LEAST-SQUARES FITTING OF RESIDUES 1 - 36 AND 46 - 115 OF EACH MONOMER. THE TWIST OF THE CENTRAL BETA SHEET OF MONOMER A IS DIFFERENT THAN THAT OF THE OTHER TWO, SO THE CHOICE OF WHICH ATOMS TO SUPERIMPOSE IS SOMEWHAT ARBITRARY. THE TRANSFORMATION PRESENTED AS *MTRIX 1* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A. THE TRANSFORMATION PRESENTED AS *MTRIX 2* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN C WHEN APPLIED TO CHAIN A. THE TRANSFORMATION PRESENTED AS *MTRIX 3* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN C WHEN APPLIED TO CHAIN B.

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Components

#1: Protein GAMMA DELTA-RESOLVASE


Mass: 15515.833 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P03012
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal grow
*PLUS
pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
240 %sat1reservoir(NH4)2SO4
340 mMTris-borate-EDTA1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→8 Å / σ(F): 1
Details: THE TURN CONSISTING OF RESIDUES 38 - 44 IN CHAIN A AND THE C-TERMINUS OF EACH CHAIN (RESIDUES A 123 - A 140, B 121 - B 140, AND C 120 - C 140) ARE DISORDERED IN THE CRYSTAL. NO COORDINATES ...Details: THE TURN CONSISTING OF RESIDUES 38 - 44 IN CHAIN A AND THE C-TERMINUS OF EACH CHAIN (RESIDUES A 123 - A 140, B 121 - B 140, AND C 120 - C 140) ARE DISORDERED IN THE CRYSTAL. NO COORDINATES ARE INCLUDED IN THIS ENTRY FOR THESE RESIDUES.
RfactorNum. reflection
obs0.2 18445
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 15 165 2863
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d1.42
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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