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- PDB-6jmg: Crystal structure of xRbj -

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Basic information

Entry
Database: PDB / ID: 6jmg
TitleCrystal structure of xRbj
ComponentsDnaJ homolog subfamily C member 27-A
KeywordsHYDROLASE / small GTPase
Function / homology
Function and homology information


GTPase activity / GTP binding / nucleus
Similarity search - Function
DnaJ domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / small GTPase Rab1 family profile. / DnaJ domain / 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 ...DnaJ domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / small GTPase Rab1 family profile. / DnaJ domain / 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 / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / DnaJ homolog subfamily C member 27-A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsGao, Z.R. / Qi, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)81773023 China
CitationJournal: To Be Published
Title: Crystal structure of Rbj
Authors: Gao, Z.R. / Qi, J.X.
History
DepositionMar 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaJ homolog subfamily C member 27-A
B: DnaJ homolog subfamily C member 27-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0906
Polymers63,9952
Non-polymers1,0954
Water25214
1
A: DnaJ homolog subfamily C member 27-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5453
Polymers31,9981
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-16 kcal/mol
Surface area14800 Å2
MethodPISA
2
B: DnaJ homolog subfamily C member 27-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5453
Polymers31,9981
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-16 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.630, 107.630, 320.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein DnaJ homolog subfamily C member 27-A / Rab and DnaJ domain-containing protein 1 / Rab and DnaJ domain-containing protein A


Mass: 31997.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: dnajc27-a, rbj-a, rbj1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7ZYF1
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 4.15 Å3/Da / Density % sol: 70.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-Tris pH 6.5, 28% (w/v) Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 31168 / % possible obs: 99.9 % / Redundancy: 19.6 % / Net I/σ(I): 30.1
Reflection shellResolution: 2.7→2.8 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.701→50 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5
RfactorNum. reflection% reflection
Rfree0.255 1542 4.96 %
Rwork0.2084 --
obs0.2108 31078 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.701→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 0 33 14 4286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094359
X-RAY DIFFRACTIONf_angle_d1.1835878
X-RAY DIFFRACTIONf_dihedral_angle_d11.622612
X-RAY DIFFRACTIONf_chiral_restr0.064626
X-RAY DIFFRACTIONf_plane_restr0.007750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7012-2.78830.30851430.26022598X-RAY DIFFRACTION100
2.7883-2.8880.37781160.26222628X-RAY DIFFRACTION100
2.888-3.00360.32081240.25742659X-RAY DIFFRACTION100
3.0036-3.14020.30611480.24792607X-RAY DIFFRACTION100
3.1402-3.30570.25891150.23342664X-RAY DIFFRACTION100
3.3057-3.51270.28321340.21962664X-RAY DIFFRACTION100
3.5127-3.78380.23831480.21342654X-RAY DIFFRACTION100
3.7838-4.16420.23731420.18582694X-RAY DIFFRACTION100
4.1642-4.7660.19631390.16762707X-RAY DIFFRACTION100
4.766-6.00170.23591670.20462743X-RAY DIFFRACTION100
6.0017-41.20690.27611660.21152918X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.6331 Å / Origin y: 32.3181 Å / Origin z: -45.4079 Å
111213212223313233
T0.4705 Å20.075 Å2-0.1242 Å2-0.546 Å2-0.1143 Å2--0.6142 Å2
L0.2412 °20.3 °2-0.017 °2-0.4714 °20.0164 °2--1.2107 °2
S0.0504 Å °-0.0067 Å °0.0358 Å °-0.0461 Å °-0.0416 Å °0.0974 Å °-0.1844 Å °-0.032 Å °-0.0168 Å °
Refinement TLS groupSelection details: all

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