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- PDB-3kye: Crystal Structure of Roadblock/LC7 Domain from Streptomyces averm... -

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Basic information

Entry
Database: PDB / ID: 3kye
TitleCrystal Structure of Roadblock/LC7 Domain from Streptomyces avermitilis
ComponentsRoadblock/LC7 domain, Robl_LC7
Keywordsstructural genomics / unknown function / alpga-beta-alpha sandwich / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology: / Dynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / Roadblock/LAMTOR2 domain-containing protein
Function and homology information
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsKim, Y. / Xu, X. / Cui, H. / Ng, J. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Roadblock/LC7 Domain from Streptomyces avermitilis
Authors: Kim, Y. / Xu, X. / Cui, H. / Ng, J. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionDec 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Roadblock/LC7 domain, Robl_LC7
B: Roadblock/LC7 domain, Robl_LC7
C: Roadblock/LC7 domain, Robl_LC7
D: Roadblock/LC7 domain, Robl_LC7


Theoretical massNumber of molelcules
Total (without water)64,7214
Polymers64,7214
Non-polymers00
Water2,756153
1
A: Roadblock/LC7 domain, Robl_LC7
B: Roadblock/LC7 domain, Robl_LC7


Theoretical massNumber of molelcules
Total (without water)32,3612
Polymers32,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-17 kcal/mol
Surface area11100 Å2
MethodPISA
2
C: Roadblock/LC7 domain, Robl_LC7
D: Roadblock/LC7 domain, Robl_LC7


Theoretical massNumber of molelcules
Total (without water)32,3612
Polymers32,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-18 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.422, 155.341, 48.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Roadblock/LC7 domain, Robl_LC7 / uncharacterized protein cvnB3


Mass: 16180.325 Da / Num. of mol.: 4 / Fragment: residues 9-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: cvnB3, SAV1632, SAV_1632 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q82MM8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 2 M ammonium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 28273 / Num. obs: 28273 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 39.9 Å2 / Rsym value: 0.111 / Net I/σ(I): 10.2
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 7 % / Mean I/σ(I) obs: 4.11 / Num. unique all: 1366 / Rsym value: 0.647 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→32.477 Å / SU ML: 0.24 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1416 5.08 %random
Rwork0.186 ---
all0.188 27847 --
obs0.188 27847 98.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.98 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.5862 Å2-0 Å20 Å2
2---17.845 Å2-0 Å2
3---11.2588 Å2
Refinement stepCycle: LAST / Resolution: 2.15→32.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3593 0 0 153 3746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133655
X-RAY DIFFRACTIONf_angle_d1.4554976
X-RAY DIFFRACTIONf_dihedral_angle_d16.0621276
X-RAY DIFFRACTIONf_chiral_restr0.096600
X-RAY DIFFRACTIONf_plane_restr0.005638
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1504-2.22720.28751270.22462536266395
2.2272-2.31630.26961250.222549267497
2.3163-2.42170.29931400.2092568270897
2.4217-2.54940.25511420.21092621276398
2.5494-2.7090.28081410.20282639278099
2.709-2.91810.25911470.19772644279199
2.9181-3.21150.25191390.20126632812100
3.2115-3.67560.23931600.175326952855100
3.6756-4.62880.17621460.151727172863100
4.6288-32.48080.19751490.18282799294897
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.84870.90030.25326.9942-1.37992.23370.11470.0272-0.0321-0.0660.0002-0.4307-0.4036-0.096-0.09860.29910.02270.04220.26340.03990.288316.70640.252811.5674
20.7743-0.3452-0.27687.7404-4.29354.2712-0.13970.2021-0.23070.08610.62930.64540.3264-0.3467-0.40680.21920.03330.03780.26680.07940.3682
31.58630.61370.58323.73511.19883.19330.06380.01440.04350.38880.06160.2478-0.0660.1171-0.11680.33280.07720.04690.21650.01130.2224
42.41611.106-0.19614.7644-0.01991.43030.17190.0492-0.16830.1246-0.00470.04970.26930.0779-0.16220.32860.0486-0.05540.26950.01030.3549
Refinement TLS groupSelection details: chain D

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