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- PDB-2gm4: An activated, tetrameric gamma-delta resolvase: Hin chimaera boun... -

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Basic information

Entry
Database: PDB / ID: 2gm4
TitleAn activated, tetrameric gamma-delta resolvase: Hin chimaera bound to cleaved DNA
Components
  • 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
  • 5'-D(*TP*TP*AP*TP*CP*GP*GP*AP*CP*AP*CP*TP*G)-3'
  • Transposon gamma-delta resolvase
KeywordsRECOMBINATION / DNA / Gamma delta resolvase / Protein DNA complex / site specific recombination
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 / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKamtekar, S. / Ho, R.S. / Li, W. / Steitz, T.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination.
Authors: Kamtekar, S. / Ho, R.S. / Cocco, M.J. / Li, W. / Wenwieser, S.V. / Boocock, M.R. / Grindley, N.D. / Steitz, T.A.
History
DepositionApr 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
Z: 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
Y: 5'-D(*TP*TP*AP*TP*CP*GP*GP*AP*CP*AP*CP*TP*G)-3'
J: 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
I: 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
K: 5'-D(*TP*TP*AP*TP*CP*GP*GP*AP*CP*AP*CP*TP*G)-3'
A: Transposon gamma-delta resolvase
B: Transposon gamma-delta resolvase


Theoretical massNumber of molelcules
Total (without water)74,3898
Polymers74,3898
Non-polymers00
Water00
1
X: 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
Z: 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
Y: 5'-D(*TP*TP*AP*TP*CP*GP*GP*AP*CP*AP*CP*TP*G)-3'
J: 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
I: 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
K: 5'-D(*TP*TP*AP*TP*CP*GP*GP*AP*CP*AP*CP*TP*G)-3'
A: Transposon gamma-delta resolvase
B: Transposon gamma-delta resolvase

X: 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
Z: 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
Y: 5'-D(*TP*TP*AP*TP*CP*GP*GP*AP*CP*AP*CP*TP*G)-3'
J: 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
I: 5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'
K: 5'-D(*TP*TP*AP*TP*CP*GP*GP*AP*CP*AP*CP*TP*G)-3'
A: Transposon gamma-delta resolvase
B: Transposon gamma-delta resolvase


Theoretical massNumber of molelcules
Total (without water)148,77816
Polymers148,77816
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Unit cell
Length a, b, c (Å)110.138, 137.687, 83.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18X
28J
19Y
29K
110I
210Z

NCS domain segments:

Dom-ID: 1

Component-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALYSLYS6AG2 - 562 - 56
21ALAALALYSLYS6BH2 - 562 - 56
12GLYGLYGLYGLY6AG58 - 7058 - 70
22GLYGLYGLYGLY6BH58 - 7058 - 70
13ASPASPASPASP6AG72 - 9472 - 94
23ASPASPASPASP6BH72 - 9472 - 94
14ASPASPILEILE2AG95 - 9795 - 97
24ASPASPILEILE2BH95 - 9795 - 97
15ASPASPALAALA6AG98 - 10298 - 102
25ASPASPALAALA6BH98 - 10298 - 102
16METMETLYSLYS6AG103 - 145103 - 145
26METMETLYSLYS6BH103 - 145103 - 145
17ILEILEASNASN6AG146 - 183146 - 183
27ILEILEASNASN6BH146 - 183146 - 183
18DADADTDT6XA3 - 192 - 18
28DADADTDT6JD3 - 192 - 18
19DTDTDCDC6YC23 - 331 - 11
29DTDTDCDC6KF23 - 331 - 11
110DADADADA6IE20 - 2219 - 21
210DADADADA6ZB20 - 2219 - 21

NCS ensembles :
IDDetails
1A B
2A B
3A B
4A B
5A B
6A B
7A B
8X J
9Y K
10I Z
DetailsThe biological assembly is a tetramer assembled using a crystallographic 2 fold axis: -x -y z

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Components

#1: DNA chain
5'-D(*CP*AP*GP*TP*GP*TP*CP*CP*GP*AP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*A)-3'


Mass: 6445.209 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*TP*AP*TP*CP*GP*GP*AP*CP*AP*CP*TP*G)-3'


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


Mass: 20337.457 Da / Num. of mol.: 2
Mutation: R2A, E56K, G96S, S98D, D100S, G101S, E102A, K105R, E124Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tnpR / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Star pLysS / References: UniProt: P03012

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN: DNA stock in 300 mM NaCl, 15 mM Tris-HCl, 0.05-0.15 M Mg Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.05 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 16189 / Num. obs: 16189 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.091
Reflection shellResolution: 3.5→3.63 Å / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1380 / % possible all: 84.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZR4

1zr4


Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 102.08 / SU ML: 0.691 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.606 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32265 802 5 %RANDOM
Rwork0.28003 ---
all0.28213 15177 --
obs0.28213 15177 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 173.333 Å2
Baniso -1Baniso -2Baniso -3
1--5.23 Å20 Å20 Å2
2---11.97 Å20 Å2
3---17.19 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 1344 0 0 4132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224309
X-RAY DIFFRACTIONr_angle_refined_deg1.1572.3596059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5825353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14623.281128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.04415571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7061534
X-RAY DIFFRACTIONr_chiral_restr0.0680.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022721
X-RAY DIFFRACTIONr_nbd_refined0.2270.21773
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22677
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2130
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.233
X-RAY DIFFRACTIONr_mcbond_it2.00221819
X-RAY DIFFRACTIONr_mcangle_it3.7642816
X-RAY DIFFRACTIONr_scbond_it2.75843255
X-RAY DIFFRACTIONr_scangle_it4.24663243
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
4A12tight positional0.030.05
4A10medium positional0.240.5
1A398loose positional0.525
2A99loose positional0.445
3A183loose positional0.395
5A32loose positional0.445
6A338loose positional0.815
7A298loose positional0.535
8X349loose positional0.515
9Y221loose positional0.345
10I63loose positional0.275
4A12tight thermal0.060.5
4A10medium thermal0.722
1A398loose thermal1.8810
2A99loose thermal5.5910
3A183loose thermal4.2110
5A32loose thermal4.5910
6A338loose thermal3.6310
7A298loose thermal2.3310
8X349loose thermal2.0510
9Y221loose thermal1.5310
10I63loose thermal2.3910
LS refinement shellResolution: 3.5→3.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 55 -
Rwork0.445 947 -
obs--86.23 %
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)
124.9609-2.1664-5.876716.97430.057318.9314-0.62-0.13831.50281.15440.32892.0292-0.1004-0.29090.2912-0.86210.33140.1333-0.99080.026-0.833592.563977.460434.5492
212.6309-3.8572-1.27937.6643-1.65930.77740.76952.4481-1.5772-1.39540.36752.08730.2623-0.7303-1.137-0.38750.1388-0.1244-0.1434-0.0508-0.198190.671168.892412.6625
346.06574.4388-5.209817.97695.966512.56280.21063.8415-0.00360.2791-0.86630.04960.5679-3.36360.65570.20710.175-1.034-0.06830.551.147256.895482.3892-1.4622
414.25622.6218-1.254223.4112-9.707714.79440.34590.78031.1283-1.3454-0.08410.0092-0.95220.0461-0.2618-0.3895-0.1630.1745-0.92060.2684-0.303112.581988.06718.74
55.32893.75943.181418.12177.1054.2450.4987-0.59910.18182.24670.3919-2.52091.22140.6713-0.8905-0.3657-0.1849-0.1829-0.74640.0139-0.081120.965986.161229.7873
615.5856-10.239417.206883.18159.657124.74391.4470.62991.5202-1.1601-1.65161.3547-1.89210.53030.2046-0.7389-0.3892-0.0916-0.5006-0.33850.2027129.9271123.389839.0383
717.6487-13.25210.345910.7-9.200310.4031-0.5803-0.97-1.11830.78272.15422.6891-1.0963-0.8477-1.57390.20970.0518-0.555-0.2210.56270.866269.694885.81446.3144
80.53373.08660.079918.66142.61635.7462-0.061-0.02250.7316-1.07360.16081.9282-0.203-0.2842-0.0998-0.6009-0.3399-0.6234-0.1286-0.24380.8066120.0428112.104933.1474
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AG1 - 1001 - 100
2X-RAY DIFFRACTION2AG101 - 145101 - 145
3X-RAY DIFFRACTION3AG146 - 183146 - 183
4X-RAY DIFFRACTION4BH2 - 1002 - 100
5X-RAY DIFFRACTION5BH101 - 145101 - 145
6X-RAY DIFFRACTION6BH146 - 183146 - 183
7X-RAY DIFFRACTION7XA2 - 191 - 18
8X-RAY DIFFRACTION7ZB20 - 2219 - 21
9X-RAY DIFFRACTION7YC23 - 351 - 13
10X-RAY DIFFRACTION8JD3 - 192 - 18
11X-RAY DIFFRACTION8IE20 - 2219 - 21
12X-RAY DIFFRACTION8KF23 - 341 - 12

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