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- PDB-2uuz: Orthorhombic crystal form of GamS from bacteriophage lambda. -

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Basic information

Entry
Database: PDB / ID: 2uuz
TitleOrthorhombic crystal form of GamS from bacteriophage lambda.
ComponentsHOST-NUCLEASE INHIBITOR PROTEIN GAM
KeywordsINHIBITOR / BACTERIOPHAGE LAMBDA / NUCLEASE INHIBITOR / RECBCD INHIBITOR / PUTATIVE DNA MIMIC
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 / MIRAS / Resolution: 2.3 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 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)142.358, 39.147, 44.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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.: 91 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 48.5 %
Crystal growpH: 8.5
Details: 100 MM TRIS/HCL, PH 8.5 32-34 % PEG 4000 700-850 MM LICL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.3→32 Å / Num. obs: 19530 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.1 / % possible all: 94.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
MLPHAREphasing
CNS1.1refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→32 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 2
Details: N-TERMINAL RESIDUES 40-48 OF CHAIN A AND 40-51 OF CHAIN B ARE DISORDERED. THE C-TERMINAL RESIDUE (VAL 138) IS DISORDERED IN BOTH CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2792 1001 4.7 %RANDOM
Rwork0.2403 ---
obs0.2403 19530 92.2 %-
Solvent computationBsol: 52.0685 Å2 / ksol: 0.347938 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.087 Å20 Å20 Å2
2---9.471 Å20 Å2
3----6.617 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 0 0 91 1540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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