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- PDB-3v4g: 1.60 Angstrom resolution crystal structure of an arginine repress... -

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Basic information

Entry
Database: PDB / ID: 3v4g
Title1.60 Angstrom resolution crystal structure of an arginine repressor from Vibrio vulnificus CMCP6
ComponentsArginine repressor
KeywordsDNA BINDING PROTEIN / arginine repressor / Vibrio vulnificus CMCP6 / virulence / type III secretion system / Center for Structural Genomics of Infectious Diseases / CSGID / TRANSCRIPTION REGULATOR
Function / homology
Function and homology information


arginine biosynthetic process / arginine binding / protein complex oligomerization / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHalavaty, A.S. / Minasov, G. / Filippova, E. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.60 Angstrom resolution crystal structure of an arginine repressor from Vibrio vulnificus CMCP6
Authors: Halavaty, A.S. / Minasov, G. / Filippova, E. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginine repressor


Theoretical massNumber of molelcules
Total (without water)19,9081
Polymers19,9081
Non-polymers00
Water3,171176
1
A: Arginine repressor
x 6


Theoretical massNumber of molelcules
Total (without water)119,4466
Polymers119,4466
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
crystal symmetry operation9_765-x+2,-x+y+1,-z1
Buried area14430 Å2
ΔGint-50 kcal/mol
Surface area34710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.308, 73.308, 118.597
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Arginine repressor


Mass: 19907.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: argR, VV0466 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/Magic / References: UniProt: Q7MP98
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: protein: 7.3 mg/mL in 10 mM Tris-HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Crystallization: The Classics II Suite (A9: 0.1 M Bis-Tris pH 5.5, 3 M NaCl). Cryo: 5M NaCl+50% sucrose, VAPOR DIFFUSION, ...Details: protein: 7.3 mg/mL in 10 mM Tris-HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Crystallization: The Classics II Suite (A9: 0.1 M Bis-Tris pH 5.5, 3 M NaCl). Cryo: 5M NaCl+50% sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97903 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2011 / Details: mirror
RadiationMonochromator: Si(111)Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 25607 / Num. obs: 25607 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 38.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 6.25 / Num. unique all: 1242 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XXB and 1F9N

1xxb

1f9n


Resolution: 1.6→29.65 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.098 / SU ML: 0.05 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19787 1300 5.1 %RANDOM
Rwork0.18164 ---
obs0.18246 24257 99.96 %-
all-24257 --
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: 23.941 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0.41 Å20 Å2
2---0.83 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 0 176 1294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221284
X-RAY DIFFRACTIONr_bond_other_d0.0010.02867
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9781750
X-RAY DIFFRACTIONr_angle_other_deg0.93632149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.5215175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.38625.45555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.8715249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.64157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
X-RAY DIFFRACTIONr_mcbond_it0.6491.5816
X-RAY DIFFRACTIONr_mcbond_other0.1521.5331
X-RAY DIFFRACTIONr_mcangle_it1.24421336
X-RAY DIFFRACTIONr_scbond_it2.0213468
X-RAY DIFFRACTIONr_scangle_it3.4084.5414
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 87 -
Rwork0.218 1741 -
obs-1741 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)
13.0981-1.2691-0.51563.7801-0.03352.14830.01030.02-0.1823-0.1297-0.0971-0.06740.09170.070.08670.05880.01120.00710.00840.01760.074644.522833.63719.3195
22.5230.25230.32852.63830.12241.61260.01680.0764-0.0302-0.06540.01820.07610.1344-0.0291-0.0350.06820.00470.01560.0067-0.00290.028239.904538.6969.9707
31.6744-1.8126-0.51053.29261.2041.0708-0.0116-0.0192-0.0858-0.010.02350.1620.0285-0.0806-0.01180.0468-0.0129-0.0010.03310.0170.018929.975953.829815.2036
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 28
2X-RAY DIFFRACTION2A29 - 83
3X-RAY DIFFRACTION3A84 - 156

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