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- PDB-2p2u: Crystal structure of putative host-nuclease inhibitor protein Gam... -

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Basic information

Entry
Database: PDB / ID: 2p2u
TitleCrystal structure of putative host-nuclease inhibitor protein Gam from Desulfovibrio vulgaris
ComponentsHost-nuclease inhibitor protein Gam, putative
KeywordsDNA BINDING PROTEIN / STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyHost-nuclease inhibitor protein Gam / Bacteriophage Mu Gam like protein / DNA protection / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / double-stranded DNA binding / Up-down Bundle / Mainly Alpha / Host-nuclease inhibitor protein Gam, putative
Function and homology information
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsBonanno, J.B. / Rutter, M. / Bain, K.T. / Zhang, F. / Romero, R. / Smith, D. / 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 putative host-nuclease inhibitor protein Gam from Desulfovibrio vulgaris
Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Zhang, F. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.6Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Host-nuclease inhibitor protein Gam, putative
B: Host-nuclease inhibitor protein Gam, putative


Theoretical massNumber of molelcules
Total (without water)38,9592
Polymers38,9592
Non-polymers00
Water70339
1
A: Host-nuclease inhibitor protein Gam, putative

A: Host-nuclease inhibitor protein Gam, putative


Theoretical massNumber of molelcules
Total (without water)38,9592
Polymers38,9592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
2
B: Host-nuclease inhibitor protein Gam, putative

B: Host-nuclease inhibitor protein Gam, putative


Theoretical massNumber of molelcules
Total (without water)38,9592
Polymers38,9592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Unit cell
Length a, b, c (Å)58.030, 93.408, 104.166
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Host-nuclease inhibitor protein Gam, putative


Mass: 19479.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Hildenborough, NCIMB 8303 / Gene: DVU_1136 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q72CZ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.62 Å3/Da / Density % sol: 66.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 9
Details: 100mM Tris-HCl pH 9.0, 21% PEG 4000, 200mM Sodium acetate, 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: Feb 24, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.75→19.976 Å / Num. all: 15027 / Num. obs: 15027 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.143 / Rsym value: 0.143 / Net I/σ(I): 12.3
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2139 / Rsym value: 0.475 / % possible all: 98.2

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→12 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.882 / SU B: 11.511 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.507 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29 767 5.2 %RANDOM
Rwork0.242 ---
obs0.245 14847 98.51 %-
all-14847 --
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 mean: 61.793 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å20 Å20 Å2
2---2.51 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.75→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 0 39 2416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222404
X-RAY DIFFRACTIONr_angle_refined_deg2.1971.9733218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.645301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9324.035114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.47615483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4481526
X-RAY DIFFRACTIONr_chiral_restr0.1440.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021754
X-RAY DIFFRACTIONr_nbd_refined0.2680.2811
X-RAY DIFFRACTIONr_nbtor_refined0.3270.21596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.271
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.2217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.235
X-RAY DIFFRACTIONr_mcbond_it1.4461.51554
X-RAY DIFFRACTIONr_mcangle_it2.00122399
X-RAY DIFFRACTIONr_scbond_it3.3633955
X-RAY DIFFRACTIONr_scangle_it5.3184.5818
LS refinement shellResolution: 2.75→2.818 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 64 -
Rwork0.31 967 -
obs-1031 98.85 %

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