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- PDB-3gwh: Crystallographic Ab Initio protein solution far below atomic reso... -

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Basic information

Entry
Database: PDB / ID: 3gwh
TitleCrystallographic Ab Initio protein solution far below atomic resolution
ComponentsTranscriptional antiterminator (BglG family)
KeywordsTRANSCRIPTION / extended helix bundle / Ab Initio / Structure solution / ARCIMBOLDO / PHASER / SHELXE
Function / homology
Function and homology information


positive regulation of DNA-templated transcription / RNA binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1950 / cAMP-dependent Protein Kinase, Chain A - #100 / Transcription antiterminator, conserved site / CAT RNA-binding domain / CAT RNA-binding domain superfamily / CAT RNA binding domain / PRD domain signature. / CAT RNA binding domain / PRD domain / PRD domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1950 / cAMP-dependent Protein Kinase, Chain A - #100 / Transcription antiterminator, conserved site / CAT RNA-binding domain / CAT RNA-binding domain superfamily / CAT RNA binding domain / PRD domain signature. / CAT RNA binding domain / PRD domain / PRD domain / PRD domain superfamily / PRD domain profile. / cAMP-dependent Protein Kinase, Chain A / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / PtsGHI operon antiterminator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 1.95 Å
AuthorsRodriguez, D.D. / Grosse, C. / Himmel, S. / Gonzalez, C. / Becker, S. / Sheldrick, G.M. / Uson, I.
CitationJournal: Nat.Methods / Year: 2009
Title: Crystallographic ab initio protein structure solution below atomic resolution
Authors: Rodriguez, D.D. / Grosse, C. / Himmel, S. / Gonzalez, C. / de Ilarduya, I.M. / Becker, S. / Sheldrick, G.M. / Uson, I.
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional antiterminator (BglG family)
B: Transcriptional antiterminator (BglG family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4994
Polymers26,3092
Non-polymers1902
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-64 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.390, 65.750, 38.190
Angle α, β, γ (deg.)90.000, 109.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcriptional antiterminator (BglG family)


Mass: 13154.480 Da / Num. of mol.: 2 / Fragment: UNP residues 178-285
Source method: isolated from a genetically manipulated source
Details: GST fusion protein, pGEX2TEV derived from commercial pGEX2T
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU13880, glcT / Plasmid: pGEX2TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O31691
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 1.77 Å3/Da / Density % sol: 30.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.4M (NH4)2SO4, 0.1M citric acid, pH6.0, vapor diffusion, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Aug 22, 2008 / Details: MULTI-LAYER INCOATEC OPTICS
RadiationMonochromator: MULTI-LAYER INCOATEC OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→35.98 Å / Num. obs: 12855 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 16.7 % / Rmerge(I) obs: 0.0906 / Net I/σ(I): 20.21
Reflection shellResolution: 1.95→2.04 Å / Redundancy: 1.75 % / Mean I/σ(I) obs: 2.45 / Num. unique all: 1786 / % possible all: 96.8

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
APEXdata collection
SAINTdata reduction
TWINABSdata scaling
Arcimboldophasing
PHASERphasing
SHELXEmodel building
RefinementMethod to determine structure: AB INITIO / Resolution: 1.95→35.98 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.185 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.837 / SU B: 4.629 / SU ML: 0.133 / SU R Cruickshank DPI: 0.214 / SU Rfree: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.214 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, The data were non-merohedrally twinned. The twinning fraction was 0.729/0.271, The data were detwinned with twinabs for refinement. The ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, The data were non-merohedrally twinned. The twinning fraction was 0.729/0.271, The data were detwinned with twinabs for refinement. The crystal was a two-component non-merohedral twin. The frames were indexed with CELL_NOW, integrated with SAINT and scaled with TWINABS (all programs from Bruker AXS) to obtain the merged intensities of the unique reflections from measurements of all 99947 reflections of domain 1, 98274 reflections of domain 2 and 25843 reflections for which both domains overlapped.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 626 4.9 %RANDOM
Rwork0.195 ---
obs0.198 12832 99.74 %-
all-24546 --
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: 59.6 Å2 / Biso mean: 27.144 Å2 / Biso min: 8.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å2-0.69 Å2
2---0.12 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 10 29 1680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221681
X-RAY DIFFRACTIONr_bond_other_d0.0020.021151
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9912276
X-RAY DIFFRACTIONr_angle_other_deg1.05832842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45624.72272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34415333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.73158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211757
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02297
X-RAY DIFFRACTIONr_mcbond_it1.1711.51003
X-RAY DIFFRACTIONr_mcbond_other0.321.5386
X-RAY DIFFRACTIONr_mcangle_it2.17221640
X-RAY DIFFRACTIONr_scbond_it3.2973678
X-RAY DIFFRACTIONr_scangle_it5.4764.5636
LS refinement shellResolution: 1.945→1.996 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 33 -
Rwork0.254 893 -
all-926 -
obs--97.58 %

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