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- PDB-1lrv: A LEUCINE-RICH REPEAT VARIANT WITH A NOVEL REPETITIVE PROTEIN STR... -

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Basic information

Entry
Database: PDB / ID: 1lrv
TitleA LEUCINE-RICH REPEAT VARIANT WITH A NOVEL REPETITIVE PROTEIN STRUCTURAL MOTIF
ComponentsLEUCINE-RICH REPEAT VARIANT
KeywordsLEUCINE-RICH REPEATS / REPETITIVE STRUCTURE / IRON SULFUR PROTEINS / NITROGEN FIXATION
Function / homology
Function and homology information


Leucine rich repeat variant / LRV FeS4 cluster / Leucine rich repeat variant / LRV protein FeS4 cluster / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.6 Å
AuthorsPeters, J.W. / Stowell, M.H.B. / Rees, D.C.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: A leucine-rich repeat variant with a novel repetitive protein structural motif.
Authors: Peters, J.W. / Stowell, M.H. / Rees, D.C.
History
DepositionNov 5, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEUCINE-RICH REPEAT VARIANT


Theoretical massNumber of molelcules
Total (without water)28,0231
Polymers28,0231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.800, 69.800, 159.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein LEUCINE-RICH REPEAT VARIANT / LRV


Mass: 28023.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Cell line: BL21
Gene: NITROGEN FIXATION SPECIFIC, OPEN READING FRAME 2 (ORF2)
Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q44534

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 70 %
Crystal growMethod: microcapillary batch diffusion / pH: 8.5
Details: THE PROTEIN WAS CRYSTALLIZED BY THE MICROCAPILLARY BATCH DIFFUSION METHOD IN 1.2 M AMMONIUM SULFATE, 1 MM SODIUM DITHIONITE BUFFERED WITH TRIS-HCL PH 8.5, microcapillary batch diffusion
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.0 Mammonium sulfate11
21 mMsodium dithionite11
3Tris-HCl11pH8.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 13656 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.3
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 3 / % possible all: 92.4
Reflection
*PLUS
Num. measured all: 63817
Reflection shell
*PLUS
% possible obs: 92.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1016 7.5 %RANDOM
Rwork0.204 ---
obs0.204 12544 92 %-
Displacement parametersBiso mean: 36.6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 8 0 1904
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.96
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.96

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