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- PDB-1zr2: Structure of a Synaptic gamma-delta Resolvase Tetramer Covalently... -

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Basic information

Entry
Database: PDB / ID: 1zr2
TitleStructure of a Synaptic gamma-delta Resolvase Tetramer Covalently Linked to two Cleaved DNAs
Components
  • AAA
  • TCAGTGTCCGATAATTTAT
  • TTATCGGACACTG
  • Transposon gamma-delta resolvase
Keywordsrecombination/DNA / resolvase / site-specific / recombination / flat interface / recombination-DNA COMPLEX
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #10 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #10 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Homeodomain-like / Helix non-globular / Homeobox-like domain superfamily / Special / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transposon gamma-delta resolvase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.9 Å
AuthorsLi, W. / Kamtekar, S. / Xiong, Y. / Sarkis, G.J. / Grindley, N.D. / Steitz, T.A.
CitationJournal: Science / Year: 2005
Title: Structure of a synaptic gamma delta resolvase tetramer covalently linked to two cleaved DNAs.
Authors: Li, W. / Kamtekar, S. / Xiong, Y. / Sarkis, G.J. / Grindley, N.D. / Steitz, T.A.
History
DepositionMay 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: TCAGTGTCCGATAATTTAT
Z: AAA
Y: TTATCGGACACTG
J: TCAGTGTCCGATAATTTAT
I: AAA
K: TTATCGGACACTG
A: Transposon gamma-delta resolvase
B: Transposon gamma-delta resolvase


Theoretical massNumber of molelcules
Total (without water)62,0498
Polymers62,0498
Non-polymers00
Water00
1
X: TCAGTGTCCGATAATTTAT
Z: AAA
Y: TTATCGGACACTG
J: TCAGTGTCCGATAATTTAT
I: AAA
K: TTATCGGACACTG
A: Transposon gamma-delta resolvase
B: Transposon gamma-delta resolvase

X: TCAGTGTCCGATAATTTAT
Z: AAA
Y: TTATCGGACACTG
J: TCAGTGTCCGATAATTTAT
I: AAA
K: TTATCGGACACTG
A: Transposon gamma-delta resolvase
B: Transposon gamma-delta resolvase


Theoretical massNumber of molelcules
Total (without water)124,09816
Polymers124,09816
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)125.050, 125.050, 127.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14X
24J
15Z
25I
16Y
26K

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAASPAG2 - 952 - 95
21ALAASPBH2 - 952 - 95
12LYSLYSAG105 - 136105 - 136
22LYSLYSBH105 - 136105 - 136
13ASNASNAG153 - 183153 - 183
23ASNASNBH153 - 183153 - 183
14DTDTXA1 - 191 - 19
24DTDTJD1 - 191 - 19
15DADAZB20 - 221 - 3
25DADAIE20 - 221 - 3
16DTDGYC23 - 351 - 13
26DTDGKF23 - 351 - 13

NCS ensembles :
ID
1
2
3
4
5
6
DetailsThe synaptic tetramer is generated by a two-fold axis: y, x, z.

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Components

#1: DNA chain TCAGTGTCCGATAATTTAT


Mass: 5809.782 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: symmetrized resolvase sites
#2: DNA chain AAA


Mass: 894.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: symmetrized resolvase sites
#3: DNA chain TTATCGGACACTG


Mass: 3966.597 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: symmetrized resolvase sites
#4: Protein Transposon gamma-delta resolvase / Transposon Tn1000 resolvase


Mass: 20353.477 Da / Num. of mol.: 2 / Mutation: R2A, E56K, G101S, E102Y, M103I, E124Q
Source method: isolated from a genetically manipulated source
Details: activated gamma-delta resolvase mutant / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tnpR / Plasmid: pSW26131 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P03012

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 4.7 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.2M Sodium Chloride, 0.1M Magnesium Formate, 0.1M Sodium Acetate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 25K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Chloride11
2Magnesium Formate11
3Sodium Acetate11
4H2O11
5Sodium Chloride12
6Magnesium Formate12
7Sodium Acetate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.909 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2003
RadiationMonochromator: Rh coated Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 3.9→41 Å / Num. all: 11577 / Num. obs: 10987 / % possible obs: 94.9 % / Observed criterion σ(F): 3.14 / Observed criterion σ(I): 1.5 / Redundancy: 3 % / Rsym value: 0.094 / Net I/σ(I): 11.9
Reflection shellHighest resolution: 3.9 Å / Redundancy: 3 % / Mean I/σ(I) obs: 11.9 / Rsym value: 0.094 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 3.9→34.5 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.811 / SU B: 125.781 / SU ML: 0.791 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.881
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.32237 1003 9.8 %RANDOM
Rwork0.26382 ---
obs0.26975 9281 100 %-
all-9694 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 97.11 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.9→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2838 1422 0 0 4260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224450
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3292.3686270
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4395363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66823.438128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.57615577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5751532
X-RAY DIFFRACTIONr_chiral_restr0.0680.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022784
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21880
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22835
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1X376medium positional0.410.5
2X128medium positional0.360.5
3X124medium positional0.220.5
1X354loose positional0.995
2X123loose positional1.015
3X119loose positional0.425
4X385loose positional0.585
5Z63loose positional0.225
6Y263loose positional0.415
LS refinement shellResolution: 3.9→4.108 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.378 128 -
Rwork0.347 1318 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
117.56114.44711.539114.4465-5.933910.09120.30060.1289-0.476-0.0360.4390.6380.163-1.2434-0.7397-0.7284-0.07270.07-0.71410.3449-0.829226.414182.06568.7592
210.01756.42598.07034.51715.80858.5442-0.67360.9732-1.2119-0.18621.00091.0285-0.26470.6256-0.3273-0.6073-0.131-0.2645-0.79020.1274-0.073434.767373.755-9.2127
334.61489.77414.926217.782111.200139.51750.9463-1.3891-1.6752-1.4682-2.12731.19790.6127-3.44531.181-0.9813-0.1725-0.7464-0.5035-0.1490.22060.084260.8601-26.4363
412.4858-2.4457.10741.17860.20757.70110.9035-1.982-0.8232-0.6637-0.41411.1392-0.7541-1.3707-0.48950.0516-0.0024-0.4515-0.10650.00990.70926.254572.4689-20.1793
512.9012.7055-4.391113.81690.74518.07190.7480.49440.4046-0.3052-0.09350.469-2.2103-0.645-0.6545-0.30440.2133-0.0485-0.77770.1084-0.995544.0669101.6854-15.6528
61.15082.61471.323226.0411.72157.97830.1984-0.14950.1691.3804-0.28640.72910.7918-0.61510.0881-0.4274-0.037-0.0813-0.87340.087-0.841948.5763101.68894.9725
723.4339-0.0258-3.484927.62794.282222.98131.41320.03211.0499-1.0046-0.4912-0.3442-1.0504-0.0084-0.922-0.4779-0.0330.027-1.5410.317-1.324845.7577142.356614.5014
84.66720.7668-1.38333.95491.93815.97890.75031.1570.622-1.2886-0.53470.1993-0.7521-0.8426-0.21560.3089-0.1497-0.0944-0.19540.3066-0.675838.1121132.19457.4795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AG1 - 991 - 99
2X-RAY DIFFRACTION2AG100 - 143100 - 143
3X-RAY DIFFRACTION3AG144 - 183144 - 183
4X-RAY DIFFRACTION4ZB20 - 221 - 3
5X-RAY DIFFRACTION4XA1 - 191 - 19
6X-RAY DIFFRACTION4YC23 - 351 - 13
7X-RAY DIFFRACTION5BH2 - 992 - 99
8X-RAY DIFFRACTION6BH100 - 143100 - 143
9X-RAY DIFFRACTION7BH144 - 183144 - 183
10X-RAY DIFFRACTION8IE20 - 221 - 3
11X-RAY DIFFRACTION8JD1 - 191 - 19
12X-RAY DIFFRACTION8KF23 - 351 - 13

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