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- PDB-2uv1: Hexagonal crystal form of GamS from bacteriophage lambda. -

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Basic information

Entry
Database: PDB / ID: 2uv1
TitleHexagonal crystal form of GamS from bacteriophage lambda.
ComponentsHOST-NUCLEASE INHIBITOR PROTEIN GAM
KeywordsINHIBITOR / PUTATIVE DNA MIMETIC / NUCLEASE INHIBITOR RECBCD INHIBITOR / BACTERIOPHAGE LAMBDA
Function / homology
Function and homology information


symbiont-mediated evasion of DNA end degradation by host / deoxyribonuclease inhibitor activity / symbiont-mediated suppression of host innate immune response
Similarity search - Function
Host-nuclease inhibitor protein Gam / Host-nuclease inhibitor Gam / Host-nuclease inhibitor Gam superfamily / Host-nuclease inhibitor protein Gam / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Host-nuclease inhibitor protein gam
Similarity search - Component
Biological speciesBACTERIOPHAGE LAMBDA (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCourt, R.I. / Cook, N. / Saikrishnan, K. / Wigley, D.B.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Crystal Structure of Lambda-Gam Protein Suggests a Model for Recbcd Inhibition.
Authors: Court, R.I. / Cook, N. / Saikrishnan, K. / Wigley, D.B.
History
DepositionMar 8, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HOST-NUCLEASE INHIBITOR PROTEIN GAM
B: HOST-NUCLEASE INHIBITOR PROTEIN GAM


Theoretical massNumber of molelcules
Total (without water)23,4662
Polymers23,4662
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.479, 84.479, 105.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein HOST-NUCLEASE INHIBITOR PROTEIN GAM / GAMS


Mass: 11733.002 Da / Num. of mol.: 2 / Fragment: RESIDUES 40-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE LAMBDA (virus) / Plasmid: PKM574 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P03702
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONSTRUCT STARTS AT RESIDUE 40 OF REPORTED SEQUENCE.

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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: 2.93 Å3/Da / Density % sol: 41.5 %
Crystal growpH: 6.5 / Details: 100 MM MES, PH 6.5, 20-25 % PEG 400, 0.1 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→73 Å / Num. obs: 6851 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 15.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 16.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UUZ

2uuz


Resolution: 2.6→105.41 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.838 / SU B: 11.503 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.564 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINAL RESIDUES 40-59 OF CHAIN A AND 40- 58 OF CHAIN B ARE DISORDERED. THE C-TERMINAL RESIDUE, VAL 138, IS DISORDERED IN BOTH CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.3 339 4.7 %RANDOM
Rwork0.235 ---
obs0.239 6911 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0.31 Å20 Å2
2---0.63 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.6→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 0 31 1323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211313
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9311760
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4115155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.61124.93881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.63615249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1841510
X-RAY DIFFRACTIONr_chiral_restr0.1050.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021016
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.2575
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2882
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6211.5812
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08321252
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.523553
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4374.5508
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
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.409 24
Rwork0.248 496

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