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- PDB-3rns: Cupin 2 conserved barrel domain protein from Leptotrichia buccalis -

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Basic information

Entry
Database: PDB / ID: 3rns
TitleCupin 2 conserved barrel domain protein from Leptotrichia buccalis
ComponentsCupin 2 conserved barrel domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG / conserved barrel domain
Function / homology
Function and homology information


Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Cupin 2 conserved barrel domain protein
Similarity search - Component
Biological speciesLeptotrichia buccalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.07 Å
AuthorsOsipiuk, J. / Tesar, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Cupin 2 conserved barrel domain protein from Leptotrichia buccalis.
Authors: Osipiuk, J. / Tesar, C. / Bearden, J. / Joachimiak, A.
History
DepositionApr 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cupin 2 conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7312
Polymers25,6721
Non-polymers591
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.684, 58.684, 143.542
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cupin 2 conserved barrel domain protein


Mass: 25672.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptotrichia buccalis (bacteria) / Strain: C-1013-b / Gene: Lebu_0116 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C7NCX6
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris-Propane:NaOH, 1.8 M sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.07→35.9 Å / Num. all: 16116 / Num. obs: 16116 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.103 / Χ2: 1.899 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.07-2.1110.90.8922.777921.338100
2.11-2.1411.80.7197541.289100
2.14-2.1912.40.758271.211100
2.19-2.2313.20.6747471.213100
2.23-2.2813.40.67921.121100
2.28-2.3313.70.487821.191100
2.33-2.3913.70.4917911.144100
2.39-2.4513.60.3517961.122100
2.45-2.5313.70.3317921.193100
2.53-2.6113.60.2937771.255100
2.61-2.713.70.2178051.3100
2.7-2.8113.60.1768081.449100
2.81-2.9413.60.1538051.664100
2.94-3.0913.60.1237991.999100
3.09-3.2913.50.0947992.251100
3.29-3.5413.30.0818072.809100
3.54-3.912.90.0758273.319100
3.9-4.4612.60.0688263.847100
4.46-5.6212.10.0578543.546100
5.62-5010.50.0619363.80798.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.07→35.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.18 / SU B: 8.636 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.151 / Phase error: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 785 4.9 %RANDOM
Rwork0.1717 ---
all0.1734 15938 --
obs0.1734 15938 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.06 Å2 / Biso mean: 43.4159 Å2 / Biso min: 24.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--1.35 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.07→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 4 61 1698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221771
X-RAY DIFFRACTIONr_bond_other_d0.0010.021200
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9742416
X-RAY DIFFRACTIONr_angle_other_deg0.88732987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.7426.3184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26215339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.425155
X-RAY DIFFRACTIONr_chiral_restr0.1070.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
X-RAY DIFFRACTIONr_mcbond_it0.9991.51088
X-RAY DIFFRACTIONr_mcbond_other0.2561.5436
X-RAY DIFFRACTIONr_mcangle_it1.82721776
X-RAY DIFFRACTIONr_scbond_it2.8193683
X-RAY DIFFRACTIONr_scangle_it4.5854.5623
LS refinement shellResolution: 2.067→2.121 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 58 -
Rwork0.235 1053 -
all-1111 -
obs-1111 96.36 %
Refinement TLS params.Method: refined / Origin x: 27.8457 Å / Origin y: 6.6124 Å / Origin z: 37.1244 Å
111213212223313233
T0.0765 Å20.016 Å20.0164 Å2-0.0735 Å20.0065 Å2--0.0848 Å2
L1.0669 °2-0.1582 °2-0.1074 °2-0.8729 °20.1371 °2--3.8103 °2
S0.1162 Å °0.0775 Å °-0.2132 Å °-0.04 Å °-0.077 Å °0.0115 Å °0.2372 Å °-0.1069 Å °-0.0392 Å °

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