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- PDB-3hzj: Crystal structure of the RabGAP domain of the RABGAP1L protein -

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Basic information

Entry
Database: PDB / ID: 3hzj
TitleCrystal structure of the RabGAP domain of the RABGAP1L protein
ComponentsRAB GTPase-activating protein 1-like
KeywordsHydrolase Activator / structural genomics consortium / GTPase activating protein / SGC / Alternative splicing / GTPase activation / Phosphoprotein / Polymorphism
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / activation of GTPase activity / GTPase activator activity / intracellular protein transport / endocytosis / regulation of protein localization / early endosome / Golgi apparatus / nucleus
Similarity search - Function
Rab GTPase-activating protein 1-like / Ypt/Rab-GAP domain of gyp1p, domain 1 / putative rabgap domain of human tbc1 domain family member 14 like domains / Ypt/Rab-GAP domain of gyp1p, domain 3 / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Kinesin-like ...Rab GTPase-activating protein 1-like / Ypt/Rab-GAP domain of gyp1p, domain 1 / putative rabgap domain of human tbc1 domain family member 14 like domains / Ypt/Rab-GAP domain of gyp1p, domain 3 / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Kinesin-like / Kinesin protein / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Cyclin A; domain 1 / Helicase, Ruva Protein; domain 3 / PH-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rab GTPase-activating protein 1-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / sad / Resolution: 2.3 Å
AuthorsNedyalkova, L. / Tempel, W. / Tong, Y. / Zhong, N. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Nedyalkova, L. / Tempel, W. / Tong, Y. / Zhong, N. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the RabGAP domain of the RABGAP1L protein
Authors: Nedyalkova, L. / Tempel, W. / Tong, Y. / Zhong, N. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAB GTPase-activating protein 1-like
B: RAB GTPase-activating protein 1-like
C: RAB GTPase-activating protein 1-like


Theoretical massNumber of molelcules
Total (without water)110,14835
Polymers110,1483
Non-polymers032
Water23413
1
A: RAB GTPase-activating protein 1-like


Theoretical massNumber of molelcules
Total (without water)36,71615
Polymers36,7161
Non-polymers014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RAB GTPase-activating protein 1-like


Theoretical massNumber of molelcules
Total (without water)36,7165
Polymers36,7161
Non-polymers04
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RAB GTPase-activating protein 1-like


Theoretical massNumber of molelcules
Total (without water)36,71615
Polymers36,7161
Non-polymers014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.086, 64.571, 290.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A591 - 797
2114B591 - 797
3114C591 - 797

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Components

#1: Protein RAB GTPase-activating protein 1-like / rabgap1l


Mass: 36716.051 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABGAP1L, HHL, KIAA0471 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q5R372
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 32 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.0539.87
2
Crystal grow
Temperature (K)Crystal-IDpHDetails
2911616% PEG3350, 0.2M potassium chloride, 1:100 (w/w) Dispase., pH 6.0, vapor diffusion, hanging drop, temperature 291K
29125.815% PEG3350, 0.2M potassium chloride, 1:100 (w/w) Dispase., pH 5.8, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCLSI 08ID-110.92015
SYNCHROTRONCLSI 08ID-120.97959
Detector
TypeIDDetectorDateDetails
MARCCD 3001CCDMay 18, 2009
MARCCD 3002CCDMay 17, 20092009-05-17
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.920151
20.979591
ReflectionRedundancy: 6.5 % / Av σ(I) over netI: 31.89 / Number: 164733 / Rmerge(I) obs: 0.079 / Χ2: 3.52 / D res high: 2.7 Å / D res low: 30 Å / Num. obs: 25196 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.83099.610.0649.2356.7
4.615.810010.0745.3477
4.034.6110010.0683.6257.2
3.664.0310010.0873.5976.9
3.43.6699.910.1112.9837.1
3.23.410010.1352.2097.2
3.043.210010.1761.617
2.913.0498.110.2161.3736.2
2.82.9193.210.271.3825.2
2.72.883.810.2951.464.4
ReflectionResolution: 2.3→30 Å / Num. obs: 38070 / % possible obs: 88.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 31.893
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.3-2.3820.23349.8
2.38-2.482.40.20665.5
2.48-2.592.80.18180.6
2.59-2.733.20.15291.9
2.73-2.93.50.11697.8
2.9-3.123.60.09299.3
3.12-3.433.80.07299.6
3.43-3.933.90.05899.7
3.93-4.954.10.0599.9
4.95-304.10.03599.3

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Phasing

PhasingMethod: sad

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVEphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 17.965 / SU ML: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED. DM, RESOLVE, CHAINSAW, RESOLVE, PHENIX, TLSMD, COOT, MOLPROBITY WERE ALSO USED FOR PHASE IMPROVEMENT AND/OR MODEL REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1191 3.128 %THIN SHELLS (SFTOOLS)
Rwork0.244 ---
obs0.245 38070 92.3 %-
Solvent computationSolvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.337 Å20 Å20 Å2
2--1.886 Å20 Å2
3----2.224 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6428 0 32 13 6473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216581
X-RAY DIFFRACTIONr_bond_other_d0.0010.024263
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.9558940
X-RAY DIFFRACTIONr_angle_other_deg0.875310364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9375827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12923.673294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.336151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1031531
X-RAY DIFFRACTIONr_chiral_restr0.0620.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027433
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021420
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_it0.3611.54137
X-RAY DIFFRACTIONr_mcbond_other0.1011.51673
X-RAY DIFFRACTIONr_mcangle_it0.70626525
X-RAY DIFFRACTIONr_scbond_it1.75432444
X-RAY DIFFRACTIONr_scangle_it2.2554.52415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2477 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.30.5
Bmedium positional0.480.5
Cmedium positional0.480.5
Amedium thermal0.462
Bmedium thermal0.432
Cmedium thermal0.482
LS refinement shellResolution: 2.3→2.36 Å
RfactorNum. reflection% reflection
Rfree0.458 57 -
Rwork0.331 1623 -
obs--57.67 %
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)
11.94850.37930.13653.5287-0.40152.66840.003-0.1316-0.0124-0.0368-0.06270.25870.0568-0.41980.05970.0722-0.0146-0.02690.179-0.02870.079633.0927-16.955548.9112
26.9652-0.77571.16922.6193-0.97184.09470.17220.1041-0.3552-0.16250.03340.12920.4662-0.979-0.20570.1085-0.11090.00740.2690.02460.04628.5802-24.772645.3552
30.9076-0.62451.34141.8055-0.68027.5177-0.25950.06970.24540.05-0.03980.0003-0.33-0.11510.29930.14080.0196-0.04190.23390.01790.131526.9395-11.630626.2821
47.89251.4996-0.38573.25941.02025.00030.0686-0.4007-1.2360.0851-0.01880.16041.218-0.5686-0.04981.0248-0.1365-0.01040.12060.14140.7698-4.2851-43.41713.7552
510.05661.3498-1.58774.58210.94651.0958-0.0252-0.8212-1.37320.3491-0.1154-0.30670.7221-0.06820.14061.00930.01450.00270.38280.2750.57381.6371-43.824317.3334
64.1858-0.3106-0.20574.3755-0.18683.7624-0.0996-0.0075-0.2877-0.0710.0880.10540.4490.22130.01160.19090.08560.0260.1913-0.01570.13298.6174-24.5317.6542
72.5766-0.9838-0.14242.7521-0.09642.95860.07440.01770.10090.2013-0.13780.1674-0.1063-0.25440.06340.0982-0.0335-0.00190.1638-0.02030.104138.2508-20.726567.0217
84.93330.70872.05085.40011.67074.92070.07540.09220.02620.2674-0.2057-0.06330.2257-0.05680.13030.1348-0.00850.0660.04150.0140.045245.6228-25.836267.2936
91.6073-0.50050.584.1378-1.94696.4001-0.0881-0.37980.04520.44310.13890.0218-0.3984-0.3475-0.05090.15890.00870.04970.11730.00580.058942.7312-24.63789.9661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A511 - 596
2X-RAY DIFFRACTION2A597 - 656
3X-RAY DIFFRACTION3A657 - 797
4X-RAY DIFFRACTION4B531 - 596
5X-RAY DIFFRACTION5B597 - 656
6X-RAY DIFFRACTION6B657 - 797
7X-RAY DIFFRACTION7C510 - 596
8X-RAY DIFFRACTION8C597 - 656
9X-RAY DIFFRACTION9C657 - 797

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