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- PDB-4drz: Crystal structure of human RAB14 -

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Basic information

Entry
Database: PDB / ID: 4drz
TitleCrystal structure of human RAB14
ComponentsRas-related protein Rab-14
KeywordsPROTEIN TRANSPORT / RAS / GTPASE / GTP / ONCOGENE / RAB14 / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


phagolysosome assembly involved in apoptotic cell clearance / phagosome maturation / Golgi to endosome transport / Golgi stack / RAB geranylgeranylation / myosin V binding / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / nuclear outer membrane-endoplasmic reticulum membrane network ...phagolysosome assembly involved in apoptotic cell clearance / phagosome maturation / Golgi to endosome transport / Golgi stack / RAB geranylgeranylation / myosin V binding / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / nuclear outer membrane-endoplasmic reticulum membrane network / tertiary granule membrane / Synthesis of PIPs at the plasma membrane / regulation of embryonic development / intracellular transport / endomembrane system / fibroblast growth factor receptor signaling pathway / rough endoplasmic reticulum / phagocytic vesicle / vesicle-mediated transport / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / trans-Golgi network / recycling endosome / recycling endosome membrane / GDP binding / regulation of protein localization / late endosome / early endosome membrane / lysosome / early endosome / defense response to bacterium / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / Neutrophil degranulation / GTP binding / perinuclear region of cytoplasm / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Ras-related protein Rab14 / 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 ...Ras-related protein Rab14 / 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-14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsWang, J. / Tempel, W. / 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 human RAB14
Authors: Wang, J. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 29, 2012ID: 2AED
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 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 1.2Sep 13, 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.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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5043
Polymers22,0211
Non-polymers4832
Water73941
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.686, 40.487, 46.486
Angle α, β, γ (deg.)90.000, 108.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ras-related protein Rab-14


Mass: 22020.910 Da / Num. of mol.: 1 / Fragment: UNP residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB14 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P61106
#2: 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.73 Å3/Da / Density % sol: 28.71 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG-3350, 0.2M CALCIUM ACETATE, pH 7.2, vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97901 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 6885 / % possible obs: 95 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.134 / Χ2: 1.195 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.382.60.4035700.995181.2
2.38-2.482.70.3726381.089186.9
2.48-2.5930.316541.062193.4
2.59-2.733.20.2777111.152197.7
2.73-2.93.40.2497031.235198.7
2.9-3.123.60.1797171.134198
3.12-3.433.60.147001.145198.7
3.43-3.933.50.17341.208199.1
3.93-4.953.40.0867191.181198.5
4.95-303.30.1157391.601197.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OIV

1oiv


Resolution: 2.3→19.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.247 / WRfactor Rwork: 0.185 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.182 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.502 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: O, XFIT, COOT AND MOLPROBITY WERE ALSO USED DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 312 4.775 %RANDOM
Rwork0.1837 ---
obs0.187 6534 95.652 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 71.6 Å2 / Biso mean: 23.708 Å2 / Biso min: 13.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.044 Å20 Å21.892 Å2
2---2.041 Å20 Å2
3---3.226 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 29 41 1309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021290
X-RAY DIFFRACTIONr_bond_other_d0.0030.02826
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9671753
X-RAY DIFFRACTIONr_angle_other_deg0.8532012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91224.48358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03415206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.919156
X-RAY DIFFRACTIONr_chiral_restr0.0660.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02269
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 (%)
2.3-2.3590.289200.19938849482.591
2.359-2.4240.364190.21537344588.09
2.424-2.4930.276250.21439145791.028
2.493-2.570.33200.19840443797.025
2.57-2.6530.335170.21539141897.608
2.653-2.7460.189130.21638740898.039
2.746-2.8480.233150.19437238999.486
2.848-2.9630.273200.21534738096.579
2.963-3.0940.285180.19434336598.904
3.094-3.2430.237150.17931833798.813
3.243-3.4160.264210.18330833398.799
3.416-3.6210.226100.17229530899.026
3.621-3.8670.182150.17227229198.625
3.867-4.1710.228170.16123925998.842
4.171-4.560.173190.14222224697.967
4.56-5.0840.24180.13921022497.321
5.084-5.8420.30880.18717820093
5.842-7.0880.37590.20515116199.379
7.088-9.7560.18620.177120122100
9.756-300.04910.2667885.897
Refinement TLS params.Method: refined / Origin x: 10.4983 Å / Origin y: 0.3775 Å / Origin z: 7.7912 Å
111213212223313233
T0.1014 Å2-0.0043 Å20.006 Å2-0.0696 Å20.0002 Å2--0.0381 Å2
L5.8722 °2-0.2741 °20.1826 °2-1.4339 °2-0.3099 °2--1.3844 °2
S0.0436 Å °-0.3596 Å °-0.0025 Å °0.0532 Å °-0.0226 Å °-0.213 Å °0.0264 Å °0.1359 Å °-0.021 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 175
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1A301 - 341

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