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- PDB-4h5j: Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12... -

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Basic information

Entry
Database: PDB / ID: 4h5j
TitleCrystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P64 form)
ComponentsGuanine nucleotide-exchange factor SEC12
KeywordsPROTEIN TRANSPORT / COPII vesicle budding / potassium binding site / beta propeller
Function / homology
Function and homology information


regulation of COPII vesicle coating / COPII-mediated vesicle transport / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / GTPase activator activity / guanyl-nucleotide exchange factor activity / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
Guanine nucleotide-exchange factor Sec12-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / Guanine nucleotide-exchange factor SEC12
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.601 Å
AuthorsMcMahon, C. / Jeffrey, P.D. / Hughson, F.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The structure of sec12 implicates potassium ion coordination in sar1 activation.
Authors: McMahon, C. / Studer, S.M. / Clendinen, C. / Dann, G.P. / Jeffrey, P.D. / Hughson, F.M.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide-exchange factor SEC12
B: Guanine nucleotide-exchange factor SEC12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6948
Polymers80,4592
Non-polymers2356
Water1,54986
1
A: Guanine nucleotide-exchange factor SEC12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3474
Polymers40,2301
Non-polymers1173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Guanine nucleotide-exchange factor SEC12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3474
Polymers40,2301
Non-polymers1173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)189.473, 189.473, 53.424
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Guanine nucleotide-exchange factor SEC12 / Protein transport protein SEC12


Mass: 40229.582 Da / Num. of mol.: 2 / Fragment: UNP residues 1-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC12, SED2, YNR026C, N3244 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11655
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.44 Å3/Da / Density % sol: 64.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.3
Details: 91 mM Tris, pH 8.0, 181 mM potassium citrate, pH 8.3, 22% w/v PEG3350, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792, 0.9794, 0.9640
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.9641
ReflectionResolution: 2.6→100 Å / Num. obs: 34159 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.12 / Χ2: 1.072 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.697.40.44634190.827199.8
2.69-2.87.60.35433630.8441100
2.8-2.937.80.28633690.868199.9
2.93-3.087.90.20833730.9081100
3.08-3.2880.15933980.995199.8
3.28-3.538.40.12334071.088199.9
3.53-3.888.90.10434131.1481100
3.88-4.459.10.0934261.2381100
4.45-5.690.07834351.3131100
5.6-1008.90.07235561.324199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
PHENIXdev_1144refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
RefinementMethod to determine structure: MAD / Resolution: 2.601→47.368 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 1.34 / Phase error: 21.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 1726 5.06 %
Rwork0.1787 --
obs0.1807 34137 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.34 Å2 / Biso mean: 34.2637 Å2 / Biso min: 4.35 Å2
Refinement stepCycle: LAST / Resolution: 2.601→47.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5261 0 6 86 5353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115355
X-RAY DIFFRACTIONf_angle_d1.1897237
X-RAY DIFFRACTIONf_chiral_restr0.081867
X-RAY DIFFRACTIONf_plane_restr0.005913
X-RAY DIFFRACTIONf_dihedral_angle_d13.6351956
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.601-2.67720.27581540.21832666282099
2.6772-2.76360.27951450.212426482793100
2.7636-2.86230.27611610.217626592820100
2.8623-2.97690.23751280.20827212849100
2.9769-3.11240.25881260.19626792805100
3.1124-3.27640.26331290.195226862815100
3.2764-3.48170.23011630.194426712834100
3.4817-3.75040.2141390.171626962835100
3.7504-4.12760.20281360.178827202856100
4.1276-4.72440.18981480.132327112859100
4.7244-5.95040.16731570.14627392896100
5.9504-47.37610.15961400.1828152955100
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)
10.0435-0.0380.0030.0263-0.0011-0.00130.02660.0493-0.1026-0.0581-0.03520.08870.0233-0.0243-0.02870.120.1823-0.1173-0.0609-0.05480.183267.503425.4956-15.6503
20.0127-0.0167-0.01270.01380.01540.0141-0.0624-0.0440.00860.03960.01040.03180.02030.0188-0.04570.30240.2179-0.00340.1946-0.01170.178464.470335.84084.2907
3-0.0005-0.0005-0.0010.00940.01250.016-0.0299-0.0327-0.05180.0870.0980.11670.0161-0.04690.08070.18060.18120.13080.07610.14110.329264.033416.10584.3182
40.00930.0037-0.00340.0048-0.0010.0020.012-0.0101-0.01170.0022-0.01250.01050.00290.0028-0.00760.19430.04230.01420.07080.01660.019593.8978-10.6315-4.6619
50.0056-0.00640.0070.0064-0.0070.0080.012-0.0203-0.02480.0147-0.0174-0.02360.00590.01090.00070.12930.028-0.00370.07980.04790.0296101.108-12.5225-0.1238
60.0134-0.00250.00480.00520.00820.00760.00890.0135-0.0155-0.07220.00660.0130.0438-0.00180.01630.25520.0212-0.02190.03710.02520.03191.9549-19.8044-20.2707
70.0006-0.0004-0.00190.00590.00380.0043-0.00190.0029-0.01250.00110.00610.0058-0.0035-0.00420.00450.2064-0.0121-0.05090.0556-0.00430.090675.905-25.7941-18.5507
80.0091-0.00260.00320.0054-0.00290.0033-0.00320.00590.0207-0.018-0.00240.00470.0314-0.0073-0.00030.1968-0.0069-0.0540.0934-0.02110.173368.3214-23.4238-13.9961
90.0080.00380.00310.00340.00690.0119-0.0235-0.01240.0036-0.0039-0.01670.0632-0.0079-0.012-0.02430.1152-0.02340.03870.0015-0.00680.154672-17.9152-1.5459
100.0006-0.0013-0.00010.00110.00090.00290.00190.00050.00920.0108-0.00750.0016-0.0022-0.0026-0.00490.1082-0.0095-0.01840.03570.03470.000786.35-11.7736-0.3779
110.00150.0003-0.0010.0008-0.00050.00170.0061-0.0145-0.0084-0.00580.00540.00290.0025-0.0106-0.00010.158-0.02540.03390.05230.03190.058684.7322-15.72087.2538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 144 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 145 through 224 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 225 through 344 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 39 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 40 through 65 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 164 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 165 through 200 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 201 through 224 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 225 through 304 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 305 through 328 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 329 through 347 )B0

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