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- PDB-3guv: Crystal structure of a resolvase family site-specific recombinase... -

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Basic information

Entry
Database: PDB / ID: 3guv
TitleCrystal structure of a resolvase family site-specific recombinase from Streptococcus pneumoniae
ComponentsSite-specific recombinase, resolvase family protein
KeywordsRECOMBINATION / STRUCTURAL GENOMICS / RECOMBINASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / DNA BINDING PROTEIN
Function / homologyResolvase, N-terminal catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Do, J. / Sampathkumar, P. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a resolvase family site-specific recombinase from Streptococcus pneumoniae
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Do, J. / Sampathkumar, P. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Site-specific recombinase, resolvase family protein


Theoretical massNumber of molelcules
Total (without water)18,8791
Polymers18,8791
Non-polymers00
Water54030
1
A: Site-specific recombinase, resolvase family protein

A: Site-specific recombinase, resolvase family protein


Theoretical massNumber of molelcules
Total (without water)37,7572
Polymers37,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2270 Å2
ΔGint-24 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.991, 46.991, 119.259
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Detailsprobable dimer

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Components

#1: Protein Site-specific recombinase, resolvase family protein


Mass: 18878.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: SP19-BS75 / Gene: CGSSp19BS75_09893 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5MQM5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 3350, 200mM zinc acetate, pH 7.0, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 12, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.2→38.519 Å / Num. all: 8257 / Num. obs: 8232 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 14.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 5.4 / Num. measured all: 7007 / Num. unique all: 1156 / Rsym value: 0.225 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.19data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.336 / WRfactor Rwork: 0.973 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.754 / SU B: 15.816 / SU ML: 0.18 / SU R Cruickshank DPI: 0.311 / SU Rfree: 0.253 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.311 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 386 4.7 %RANDOM
Rwork0.226 ---
obs0.229 8180 99.5 %-
all-8221 --
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 max: 62.08 Å2 / Biso mean: 34.29 Å2 / Biso min: 13.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20.8 Å20 Å2
2--1.6 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 0 0 30 1173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221152
X-RAY DIFFRACTIONr_bond_other_d0.0010.02786
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9691543
X-RAY DIFFRACTIONr_angle_other_deg0.94231919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4995147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55524.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8115221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.729158
X-RAY DIFFRACTIONr_chiral_restr0.080.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021276
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
X-RAY DIFFRACTIONr_mcbond_it0.8661.5733
X-RAY DIFFRACTIONr_mcbond_other0.1771.5307
X-RAY DIFFRACTIONr_mcangle_it1.61621169
X-RAY DIFFRACTIONr_scbond_it2.6153419
X-RAY DIFFRACTIONr_scangle_it4.5034.5374
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 28 -
Rwork0.305 563 -
all-591 -
obs-563 100 %
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)
12.2922-0.68740.20981.1127-0.5211.10020.27760.03130.0159-0.1603-0.20360.05970.01410.1684-0.0740.07840.0382-0.02250.061-0.03040.02218.97411.95999.5627
21.44033.6236-1.61179.1778-4.18372.26450.0410.0564-0.01120.11130.11680.0196-0.1156-0.0583-0.15770.0660.02220.00490.0254-0.00570.070410.310718.4949-8.1307
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 120
2X-RAY DIFFRACTION2A125 - 151

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