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- PDB-2il1: Crystal structure of a predicted human GTPase in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 2il1
TitleCrystal structure of a predicted human GTPase in complex with GDP
ComponentsRab12
KeywordsPROTEIN TRANSPORT / G-PROTEIN / RAB / GDP / GTPASE / PREDICTED / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


retrograde transport, plasma membrane to Golgi / protein catabolic process => GO:0030163 / Rab protein signal transduction / phagosome maturation / Retrograde transport at the Trans-Golgi-Network / insulin-responsive compartment / RAB geranylgeranylation / vesicle docking involved in exocytosis / regulation of exocytosis / RAB GEFs exchange GTP for GDP on RABs ...retrograde transport, plasma membrane to Golgi / protein catabolic process => GO:0030163 / Rab protein signal transduction / phagosome maturation / Retrograde transport at the Trans-Golgi-Network / insulin-responsive compartment / RAB geranylgeranylation / vesicle docking involved in exocytosis / regulation of exocytosis / RAB GEFs exchange GTP for GDP on RABs / virion assembly / endosome to lysosome transport / Golgi organization / positive regulation of macroautophagy / autophagosome assembly / protein secretion / autophagosome / endomembrane system / phagocytic vesicle / trans-Golgi network membrane / protein localization to plasma membrane / intracellular protein transport / recycling endosome / autophagy / cellular response to type II interferon / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / synaptic vesicle / lysosome / endosome / lysosomal membrane / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Rab12 / : / 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 ...Rab12 / : / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-12 / Ras-related protein Rab-43
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsWang, J. / Shen, Y. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of a predicted human GTPase in complex with GDP
Authors: Wang, J. / Shen, Y. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionOct 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT OF THE PROTEIN IS NOT KNOWN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rab12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,43810
Polymers21,9301
Non-polymers5089
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Rab12
hetero molecules

A: Rab12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,87620
Polymers43,8602
Non-polymers1,01518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2990 Å2
ΔGint-72 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.463, 45.463, 315.454
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-501-

CA

21A-1004-

HOH

Detailsnot known

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Rab12


Mass: 21930.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Rab12 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE-3)-RIL / References: UniProt: Q86YS6, UniProt: Q6IQ22*PLUS

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Non-polymers , 5 types, 33 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.5 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 22% PEG4000, 0.2M calcium acetate, 0.1M sodium cacodylate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 13543 / % possible obs: 94.2 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.052 / Χ2: 1.218 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID
2-2.0752.32.10.437301.6051
2.07-2.1591.54.90.31412430.5751
2.15-2.2598.89.90.26613600.6331
2.25-2.3799.614.50.20713860.5661
2.37-2.5210016.90.15313980.5771
2.52-2.7110017.80.10514010.6971
2.71-2.9910017.70.07914201.0341
2.99-3.4299.717.30.05214581.4011
3.42-4.3199.916.20.04714752.1751
4.31-5098.614.30.03916722.4391

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å39.35 Å
Translation2.5 Å39.35 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT1.701data extraction
HKL-2000data scaling
REFMAC5.2.0019refinement
ARP/wARPmodel building
MolProbitymodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G17, chain A

1g17


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.246 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.24 / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2661 615 4.994 %
Rwork0.2412 --
obs-12316 99.467 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.449 Å2
Baniso -1Baniso -2Baniso -3
1--0.056 Å2-0.028 Å20 Å2
2---0.056 Å20 Å2
3---0.085 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 36 24 1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221344
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9911817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48324.82156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40715252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.609157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02966
X-RAY DIFFRACTIONr_nbd_refined0.2060.2562
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2945
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.254
X-RAY DIFFRACTIONr_metal_ion_refined0.2210.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0920.21
X-RAY DIFFRACTIONr_mcbond_it2.4392853
X-RAY DIFFRACTIONr_mcangle_it3.24531324
X-RAY DIFFRACTIONr_scbond_it2.742584
X-RAY DIFFRACTIONr_scangle_it3.63491
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1540.328420.28380088495.249
2.154-2.2130.283520.24976783298.438
2.213-2.2770.343490.23981686699.885
2.277-2.3470.266360.23774578299.872
2.347-2.4230.321350.226751786100
2.423-2.5070.304390.239751790100
2.507-2.6010.341350.237679714100
2.601-2.7070.227450.23676721100
2.707-2.8260.227290.248679708100
2.826-2.9630.271270.235617644100
2.963-3.1210.342390.225599638100
3.121-3.3080.272320.24558862199.839
3.308-3.5340.32210.2254857199.65
3.534-3.8120.22310.21516547100
3.812-4.170.258240.22478502100
4.17-4.6510.2300.20143546799.572
4.651-5.3490.162130.23396409100
5.349-6.4990.27150.301370385100
6.499-8.9830.353120.293291303100
8.983-300.29790.32319921298.113
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)
11.6386-0.2771-0.42211.94270.58484.9988-0.02410.34240.03140.0954-0.1986-0.088-0.1169-0.21050.2227-0.2301-0.0138-0.0221-0.0191-0.1146-0.0763.809523.246111.3459
24.9557-6.21156.23514.27460.768919.20010.74460.1702-0.28731.0879-0.28160.89370.4352-0.767-0.463-0.1618-0.25220.07270.2999-0.32490.0993-7.514616.339913.9992
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A134 - 30422 - 192
22D4011

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