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- PDB-2gm5: An activated, truncated gamma-delta resolvase tetramer -

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Basic information

Entry
Database: PDB / ID: 2gm5
TitleAn activated, truncated gamma-delta resolvase tetramer
ComponentsTransposon gamma-delta resolvase
KeywordsRECOMBINATION / GAMMA DELTA RESOLVASE / SITE SPECIFIC RECOMBINATION
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 domain ...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 / SYNCHROTRON / MAD / Resolution: 2.1 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 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transposon gamma-delta resolvase
B: Transposon gamma-delta resolvase
C: Transposon gamma-delta resolvase
D: Transposon gamma-delta resolvase


Theoretical massNumber of molelcules
Total (without water)62,7704
Polymers62,7704
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-40 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.331, 98.476, 100.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological ssembly is a tetramer in the asymmetric unit

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Components

#1: Protein
Transposon gamma-delta resolvase / Transposon Tn1000 resolvase


Mass: 15692.408 Da / Num. of mol.: 4 / Mutation: R2A, E56K, G101S, E102Y, M103I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tnpR / Plasmid: pET derived / Production host: Escherichia coli (E. coli) / Strain (production host): B834DE3 / References: UniProt: P03012
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein in 200 mM NaCl, 3.75 mM DTT, 40 mM Tris-HCl, 0.05 M Li2SO4, 7.5% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97180, 0.97930, 0.97950
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 3, 2003
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97181
20.97931
30.97951
ReflectionRedundancy: 3.8 % / Av σ(I) over netI: 7.7 / Number: 226705 / Rmerge(I) obs: 0.089 / Χ2: 1.03 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 59517 / % possible obs: 99.8
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
4.5250590298.70.0281.0533.9
3.594.52594999.90.0421.0243.7
3.143.5959531000.0821.0633.8
2.853.1460001000.1251.0483.8
2.652.8559221000.1931.0193.8
2.492.6559881000.2831.013.8
2.372.4959641000.3641.0023.8
2.262.3759361000.4781.0173.8
2.182.26598199.90.6371.0833.8
2.12.1859221000.7381.0333.8
ReflectionResolution: 2.1→50 Å / Num. all: 59517 / Num. obs: 59517 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.089 / Χ2: 1.035 / Net I/σ(I): 7.7
Reflection shellResolution: 2.1→2.18 Å / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5922 / Num. unique obs: 5922 / Χ2: 1.033 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→47.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.934 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3122 9.9 %RANDOM
Rwork0.215 ---
all0.219 31507 --
obs0.219 31507 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.817 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å20 Å20 Å2
2---0.56 Å20 Å2
3---2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 0 147 3817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223689
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.9814928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2595458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25623.576165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35215748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6751539
X-RAY DIFFRACTIONr_chiral_restr0.0610.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022627
X-RAY DIFFRACTIONr_nbd_refined0.1790.21653
X-RAY DIFFRACTIONr_nbtor_refined0.2910.22536
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2176
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.218
X-RAY DIFFRACTIONr_mcbond_it1.0981.52401
X-RAY DIFFRACTIONr_mcangle_it1.53723688
X-RAY DIFFRACTIONr_scbond_it2.65331425
X-RAY DIFFRACTIONr_scangle_it4.1744.51240
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 223 -
Rwork0.258 2051 -
obs-2274 99.96 %
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)
15.20320.533-0.88657.6172-1.05335.3137-0.0909-0.665-0.12290.5688-0.1132-0.4242-0.01020.3160.2041-0.1620.0009-0.0098-0.1378-0.0059-0.113512.332522.162425.6756
25.49970.3089-0.05045.54120.40538.0505-0.02790.89480.0629-0.47150.0430.1642-0.11710.1314-0.0151-0.13960.0243-0.0452-0.0141-0.0645-0.176852.51132.20116.1284
36.131-1.47321.00364.94580.09997.5105-0.0486-0.7503-0.24510.73520.00070.27050.3502-0.20970.0479-0.0869-0.00950.0313-0.1384-0.0235-0.125546.160645.672732.6593
48.0019-0.63731.48687.45760.46974.75370.020.40320.4448-0.64040.0756-0.4621-0.32730.2779-0.0956-0.1086-0.01780.0613-0.1276-0.015-0.045517.789353.889316.2241
517.8667-8.547211.29588.3729-6.893712.8973-0.0338-0.3675-0.23090.2662-0.1057-0.55070.16440.1030.1395-0.1381-0.07540.0415-0.2361-0.0454-0.112234.636225.205723.7641
619.9329-5.530911.78677.6765-4.090113.9965-0.0120.864-0.1916-0.3938-0.15190.0607-0.3776-0.09420.1639-0.1689-0.02520.0654-0.2008-0.0945-0.179234.63230.756212.5212
725.12328.5265-17.50948.5508-6.19318.39750.488-1.1025-0.22910.4889-0.57820.4479-0.20960.19540.0903-0.2255-0.0181-0.0459-0.1918-0.1035-0.129332.519637.378526.0724
817.93785.8737-12.46669.2977-7.618518.45640.29650.58160.2035-0.2597-0.5146-0.4412-0.44870.2330.2181-0.19850.0469-0.0446-0.1954-0.035-0.124532.009343.745114.192
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 991 - 98
22BB2 - 991 - 98
33CC2 - 991 - 98
44DD2 - 991 - 98
55AA100 - 12899 - 127
66BB100 - 12399 - 122
77CC100 - 12599 - 124
88DD100 - 12799 - 126

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