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- PDB-3nkv: Crystal structure of Rab1b covalently modified with AMP at Y77 -

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Basic information

Entry
Database: PDB / ID: 3nkv
TitleCrystal structure of Rab1b covalently modified with AMP at Y77
ComponentsRas-related protein Rab-1B
KeywordsPROTEIN TRANSPORT / posttranslational modification / AMPylation / adenylylation / Rab1b / vesicular transport
Function / homology
Function and homology information


positive regulation of glycoprotein metabolic process / RAB geranylgeranylation / phagophore assembly site membrane / regulation of autophagosome assembly / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / Golgi organization ...positive regulation of glycoprotein metabolic process / RAB geranylgeranylation / phagophore assembly site membrane / regulation of autophagosome assembly / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / Golgi organization / autophagosome assembly / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / small monomeric GTPase / intracellular protein transport / G protein activity / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / cytosol
Similarity search - Function
: / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain ...: / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsMueller, M.P. / Peters, H. / Blankenfeldt, W. / Goody, R.S. / Itzen, A.
CitationJournal: Science / Year: 2010
Title: The Legionella effector protein DrrA AMPylates the membrane traffic regulator Rab1b.
Authors: Muller, M.P. / Peters, H. / Blumer, J. / Blankenfeldt, W. / Goody, R.S. / Itzen, A.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-1B
B: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,56710
Polymers39,5052
Non-polymers2,0628
Water4,414245
1
A: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7835
Polymers19,7521
Non-polymers1,0314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7835
Polymers19,7521
Non-polymers1,0314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.970, 100.589, 45.071
Angle α, β, γ (deg.)90.00, 102.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ras-related protein Rab-1B


Mass: 19752.369 Da / Num. of mol.: 2 / Fragment: Rab1b-AMP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1B, RAB1B_HUMAN / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9H0U4

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Non-polymers , 5 types, 253 molecules

#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 298 K / pH: 6
Details: 15% (v/v) isopropanol, 15% (w/v) PEG4000, 0.1 M imidazole, 10 mM BaCl2, pH 6.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786
DetectorType: PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2010 / Details: SI(111)
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.7→19.8 Å / Num. obs: 33392 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.8
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementResolution: 1.7→19.8 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.83 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18686 1658 5 %RANDOM
Rwork0.14958 ---
obs0.1515 31709 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.283 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-1.45 Å2
2---1.4 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2701 0 112 245 3058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222891
X-RAY DIFFRACTIONr_bond_other_d0.0010.021914
X-RAY DIFFRACTIONr_angle_refined_deg2.0532.0043930
X-RAY DIFFRACTIONr_angle_other_deg1.0634674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98124.488127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40515517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5471516
X-RAY DIFFRACTIONr_chiral_restr0.1290.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02595
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3951.51685
X-RAY DIFFRACTIONr_mcbond_other0.4751.5697
X-RAY DIFFRACTIONr_mcangle_it2.42122723
X-RAY DIFFRACTIONr_scbond_it3.6231204
X-RAY DIFFRACTIONr_scangle_it5.7264.51197
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 129 -
Rwork0.193 2366 -
obs--99.88 %
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)
11.5080.48460.19431.0420.47991.7764-0.12450.0693-0.02420.02320.113-0.00520.0805-0.03190.01150.02440.0050.01370.0458-0.00930.039-3.26321.883-2.405
21.0081-0.32330.08890.8355-0.14151.19730.11290.0017-0.1193-0.133-0.02530.0239-0.02450.0228-0.08760.0439-0.01050.00840.027500.049-4.587-6.169-19.716
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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