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- PDB-4bqq: Protein crystal structure of the N-terminal and recombinase domai... -

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Basic information

Entry
Database: PDB / ID: 4bqq
TitleProtein crystal structure of the N-terminal and recombinase domains of the Streptomyces temperate phage serine recombinase, fC31 integrase.
ComponentsINTEGRASE
KeywordsHYDROLASE / SERINE RECOMBINASE / UNIDIRECTIONAL / SITE-SPECIFIC RECOMBINATION
Function / homology
Function and homology information


DNA strand exchange activity / peptidase activity / DNA binding
Similarity search - Function
Putative Large Serine Recombinase; Chain B, Domain 2 / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / Hect, E3 ligase catalytic domain fold / Resolvase, N-terminal catalytic domain / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain ...Putative Large Serine Recombinase; Chain B, Domain 2 / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / Hect, E3 ligase catalytic domain fold / Resolvase, N-terminal catalytic domain / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSTREPTOMYCES PHAGE PHIC31 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsMcMahon, S.A. / McEwan, A.R. / Smith, M.C.M. / Naismith, J.H.
CitationJournal: To be Published
Title: Protein Crystal Structure of the N-Terminal and Recombinase Domains of the Streptomyces Temperate Phage Serine Recombinase, Fc31 Integrase.
Authors: McMahon, S.A. / McEwan, A.R. / Smith, M.C.M. / Naismith, J.H.
History
DepositionMay 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTEGRASE
B: INTEGRASE


Theoretical massNumber of molelcules
Total (without water)88,8212
Polymers88,8212
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-32.8 kcal/mol
Surface area35260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.040, 96.040, 117.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 369 / Label seq-ID: 26 - 394

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.9176, 0.3742, -0.134), (0.3841, 0.7479, -0.5414), (-0.1024, -0.5483, -0.83)
Vector: 8.8331, 34.5982, 116.6098)

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Components

#1: Protein INTEGRASE


Mass: 44410.395 Da / Num. of mol.: 2
Fragment: RESOLVASE N-TERMINAL AND RECOMBINASE DOMAIN, RESIDUES 1 -371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES PHAGE PHIC31 (virus) / Plasmid: PEHISTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9T221
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 3.06 Å3/Da / Density % sol: 59.8 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1M SODIUM CITRATE PH5.5, 1.55M DI AMMONIUM HYDROGEN PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→96.04 Å / Num. obs: 56465 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.1
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.6 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0111refinement
xia2data reduction
xia2data scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.15→96.04 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 11.366 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24427 2865 5.1 %RANDOM
Rwork0.2183 ---
obs0.21963 53600 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.885 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.15→96.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 0 185 5453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225398
X-RAY DIFFRACTIONr_bond_other_d0.0030.023869
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9667286
X-RAY DIFFRACTIONr_angle_other_deg0.97839331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4585671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77822.51251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20915960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3761564
X-RAY DIFFRACTIONr_chiral_restr0.0710.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215989
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021139
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12005 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.154→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 192 -
Rwork0.314 3858 -
obs--97.24 %
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)
13.58111.3927-0.73147.7694-1.61893.68310.3219-0.5006-0.26480.4473-0.7795-0.16890.20040.38350.45760.3129-0.08510.03870.42540.03430.086819.55948.94623.907
24.2232.66211.80932.25731.84251.728-0.48840.1341-0.7695-0.77260.4513-0.3268-0.80330.28330.03710.7989-0.19470.06280.6921-0.14920.558829.65263.38741.992
34.90755.4315-2.68357.48-1.54353.7279-0.25930.0439-1.7342-0.43350.2209-1.8878-0.06960.22510.03840.33670.04550.06750.40690.06131.693435.91844.6849.031
417.45252.9108-2.68435.7097.288211.9404-0.0141-1.3963-2.10710.83860.1967-0.82481.010.8437-0.18261.01440.1161-0.47410.87170.57011.79231.89934.03666.213
56.58132.6069-0.03427.394-1.94131.1243-0.036-0.7925-0.87671.0121-0.1748-1.3822-0.3664-0.11990.21080.45630.0218-0.13140.360.08410.325721.23649.49655.735
62.14140.0985-0.13472.50750.20872.8826-0.1814-0.18690.6385-0.1086-0.19210.78-0.4712-0.27750.37350.23780.0385-0.15610.2274-0.17330.47095.88671.35910.589
72.5112-3.54030.742110.541-1.36540.8127-0.35560.11570.01260.16840.35540.4308-0.0473-0.33550.00020.27920.02480.11010.52750.16080.2464-13.71254.47246.82
811.94525.0886-3.20458.519-5.02819.99740.12980.4179-0.7086-0.38790.37810.14870.6522-1.1125-0.50790.2986-0.2062-0.13530.5408-0.03890.4267-15.96436.1639.099
93.49410.2746-0.09891.3715-0.91192.4379-0.00220.4247-0.0082-0.13360.1880.1782-0.2336-0.1044-0.18570.3035-0.02220.08190.30530.05150.08660.23849.23440.69
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 132
2X-RAY DIFFRACTION2A133 - 174
3X-RAY DIFFRACTION3A175 - 227
4X-RAY DIFFRACTION4A240 - 260
5X-RAY DIFFRACTION5A272 - 369
6X-RAY DIFFRACTION6B1 - 170
7X-RAY DIFFRACTION7B171 - 227
8X-RAY DIFFRACTION8B242 - 260
9X-RAY DIFFRACTION9B270 - 370

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