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- PDB-2o52: Crystal structure of human RAB4B in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 2o52
TitleCrystal structure of human RAB4B in complex with GDP
ComponentsRas-related protein Rab-4B
KeywordsPROTEIN TRANSPORT / G-PROTEIN / RAB / GDP / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


Rab protein signal transduction / neutrophil degranulation / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / glucose import / regulation of endocytosis / secretory granule membrane / recycling endosome / protein transport ...Rab protein signal transduction / neutrophil degranulation / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / glucose import / regulation of endocytosis / secretory granule membrane / recycling endosome / protein transport / endosome / GTPase activity / Neutrophil degranulation / GTP binding / perinuclear region of cytoplasm / plasma membrane
Similarity search - Function
Rab4 / small GTPase Rab1 family profile. / Small GTPase / Ras family / 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
BETA-MERCAPTOETHANOL / GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsZhu, H. / Tempel, W. / Wang, J. / Shen, Y. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. ...Zhu, H. / Tempel, W. / Wang, J. / Shen, Y. / 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 human RAB4B in complex with GDP
Authors: Zhu, H. / Tempel, W. / Wang, J. / Shen, Y. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionDec 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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.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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300Author states that biological unit for the protein is not yet known
Remark 999Sequence These are from isoform 2: P61018-2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-4B
B: Ras-related protein Rab-4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7649
Polymers44,6722
Non-polymers1,0917
Water1,35175
1
A: Ras-related protein Rab-4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8825
Polymers22,3361
Non-polymers5464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Rab-4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8824
Polymers22,3361
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.528, 67.528, 179.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsnot known

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ras-related protein Rab-4B


Mass: 22336.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB4B / Plasmid: p28a-thrombin-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE-3)-RIL / References: UniProt: P61018

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Non-polymers , 5 types, 82 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.295 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG8000, 0.2M magnesium acetate, 0.1M sodium cacodylate, pH 6.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 40474 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.119 / Χ2: 1.936 / Net I/σ(I): 9
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
2.2-2.2810060.97640441.498
2.28-2.3710060.90940471.555
2.37-2.4810060.7240421.588
2.48-2.611006.10.52140611.636
2.61-2.771006.10.43140221.73
2.77-2.991006.20.26940401.827
2.99-3.291006.20.16140562.1
3.29-3.761006.30.09640472.296
3.76-4.731006.40.06240422.597
4.73-301006.60.04840732.406

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
ARP/wARPmodel building
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2bme

2bme


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.187 / SU B: 5.688 / SU ML: 0.148 / ESU R: 0.247 / ESU R Free: 0.217 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 1033 4.739 %thin shells
Rwork0.2135 ---
all0.216 ---
obs-21799 99.177 %-
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: 33.089 Å2
Baniso -1Baniso -2Baniso -3
1-1.466 Å20 Å20 Å2
2--1.466 Å20 Å2
3----2.932 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 63 75 2676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222651
X-RAY DIFFRACTIONr_bond_other_d0.0020.021762
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9833593
X-RAY DIFFRACTIONr_angle_other_deg0.9073.0014280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4315331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85123.86114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35815445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0321517
X-RAY DIFFRACTIONr_chiral_restr0.0790.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022917
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02564
X-RAY DIFFRACTIONr_nbd_refined0.1980.2503
X-RAY DIFFRACTIONr_nbd_other0.1930.21738
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21277
X-RAY DIFFRACTIONr_nbtor_other0.0870.21364
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2990.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.29
X-RAY DIFFRACTIONr_mcbond_it2.45621677
X-RAY DIFFRACTIONr_mcbond_other0.6532671
X-RAY DIFFRACTIONr_mcangle_it3.66332597
X-RAY DIFFRACTIONr_scbond_it2.39421143
X-RAY DIFFRACTIONr_scangle_it3.2563991
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.2-2.25600.23915920.239159799.687
2.256-2.3170.3442180.24613010.259152699.541
2.317-2.38400.24514640.245147399.389
2.384-2.45600.24314510.243145699.657
2.456-2.5350.2641810.22312150.229140599.359
2.535-2.62300.22713620.227136799.634
2.623-2.720.3391560.24311580.254133198.723
2.72-2.82900.23612690.236128598.755
2.829-2.95200.2312120.23122399.101
2.952-3.0930.2941170.22410570.231119298.49
3.093-3.25600.22611030.226111499.013
3.256-3.4470.275960.2039720.209107998.981
3.447-3.67800.21110010.211101598.621
3.678-3.9610.266760.1928650.19895099.053
3.961-4.3220.229680.1928000.19588897.748
4.322-4.80400.1688080.16881998.657
4.804-5.4950.19450.1916800.19172799.725
5.495-6.6070.296320.2456080.248640100
6.607-8.8720.284210.2115040.21452699.81
8.872-200.229230.2213440.222367100

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