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- PDB-2pmy: EF-hand domain of human RASEF -

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Basic information

Entry
Database: PDB / ID: 2pmy
TitleEF-hand domain of human RASEF
ComponentsRAS and EF-hand domain-containing protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Rasef / EFH / calcium-binding domain / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


vesicle-mediated transport / GDP binding / GTPase activity / calcium ion binding / GTP binding / perinuclear region of cytoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / EF-hand / Recoverin; domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / EF-hand domain pair / Rab subfamily of small GTPases ...small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / EF-hand / Recoverin; domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / EF-hand domain pair / Rab subfamily of small GTPases / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ras and EF-hand domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / sad / Resolution: 2.3 Å
AuthorsZhu, H. / Shen, Y. / Wang, J. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. ...Zhu, H. / Shen, Y. / Wang, J. / 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: EF-hand domain of human RASEF
Authors: Zhu, H. / Shen, Y. / Wang, J. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: 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
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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_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_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 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS and EF-hand domain-containing protein
B: RAS and EF-hand domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,89111
Polymers20,6352
Non-polymers2569
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-46 kcal/mol
Surface area7790 Å2
MethodPISA
2
A: RAS and EF-hand domain-containing protein
hetero molecules

A: RAS and EF-hand domain-containing protein
hetero molecules

B: RAS and EF-hand domain-containing protein
hetero molecules

B: RAS and EF-hand domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,78222
Polymers41,2694
Non-polymers51318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
crystal symmetry operation5_545-x+1/2,y-1/2,-z+3/41
Buried area4490 Å2
ΔGint-80 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.259, 61.259, 101.598
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

#1: Protein RAS and EF-hand domain-containing protein


Mass: 10317.351 Da / Num. of mol.: 2 / Fragment: EF-hand domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: MuscleSkeletal muscle / Gene: RASEF, RP11-158H18.1-001 / Plasmid: pET28mhl(TEV) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon(+)RIL / References: UniProt: Q8IZ41
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5
Details: 0.6M Ammonium sulfate, 0.1M Sodium cacodylate, 0.01M Magnesium chloride, pH 5.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 17, 2007
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: 18809 / % possible obs: 100 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.137 / Χ2: 1.876 / Net I/σ(I): 8
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Num. unique obsΧ2Rmerge(I) obs
2.2-2.2810014.518891.505
2.28-2.3710014.718851.4520.953
2.37-2.4810014.818711.510.759
2.48-2.6110014.918701.5480.579
2.61-2.771001518731.660.396
2.77-2.991001518891.6990.308
2.99-3.2910015.118791.8870.19
3.29-3.7610015.218762.2550.108
3.76-4.7310015.218902.4370.065
4.73-3099.514.418872.8010.053

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Phasing

PhasingMethod: sad
Phasing MADD res high: 3.2 Å / D res low: 20 Å / FOM : 0.37 / Reflection: 3449
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Ca30.3550.9230.7880.0971.699
2Ca40.1210.2050.9930.0071.914
3Ca600.0550.9860.0721.304
4Ca43.380.3820.5590.0850.895
Phasing MAD shell
Resolution (Å)FOM Reflection
10.43-200.32217
6.96-10.430.4308
5.55-6.960.42371
4.75-5.550.43431
4.22-4.750.38472
3.83-4.220.39508
3.54-3.830.35553
3.3-3.540.3589
Phasing dmFOM : 0.63 / FOM acentric: 0.63 / FOM centric: 0.61 / Reflection: 7139 / Reflection acentric: 5627 / Reflection centric: 1512
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-19.9230.890.930.84345183162
4.5-7.10.860.890.78992705287
3.6-4.50.860.880.761208932276
3.1-3.60.750.780.641191967224
2.7-3.10.480.490.4421061744362
2.5-2.70.280.280.2612971096201

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.11phasing
RESOLVE2.11phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.203 / ESU R: 0.282 / ESU R Free: 0.224
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Resolve, arp/warp, coot, molprobity programs were also used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 494 5.432 %Thin shells
Rwork0.2286 ---
all0.23 ---
obs-9095 99.89 %-
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: 28.406 Å2
Baniso -1Baniso -2Baniso -3
1-0.354 Å20 Å20 Å2
2--0.354 Å20 Å2
3----0.708 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 13 15 1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211120
X-RAY DIFFRACTIONr_bond_other_d00.02793
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.971503
X-RAY DIFFRACTIONr_angle_other_deg4.30631883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8615143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.00522.45961
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22615182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1111517
X-RAY DIFFRACTIONr_chiral_restr0.0710.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021308
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02269
X-RAY DIFFRACTIONr_nbd_refined0.3130.2294
X-RAY DIFFRACTIONr_nbd_other0.2230.2751
X-RAY DIFFRACTIONr_nbtor_refined0.170.2581
X-RAY DIFFRACTIONr_nbtor_other0.10.2528
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.216
X-RAY DIFFRACTIONr_metal_ion_refined0.290.219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3560.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.26
X-RAY DIFFRACTIONr_mcbond_it2.3772715
X-RAY DIFFRACTIONr_mcbond_other02298
X-RAY DIFFRACTIONr_mcangle_it3.68531116
X-RAY DIFFRACTIONr_scbond_it2.5422405
X-RAY DIFFRACTIONr_scangle_it3.7573387
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 (%)
2.3-2.3590.327430.2686120.27265699.848
2.359-2.4240.301660.2435570.25623100
2.424-2.49300.2616120.261612100
2.493-2.570.298470.2485660.252613100
2.57-2.65300.245870.24587100
2.653-2.7460.271470.265090.261556100
2.746-2.8480.317320.2355190.239551100
2.848-2.9640.4280.2415200.244528100
2.964-3.0940.281450.2454720.24951999.615
3.094-3.2430.343310.2454570.25148999.796
3.243-3.41600.2284700.228470100
3.416-3.6210.237380.2064140.208452100
3.621-3.8670.135210.2123870.208408100
3.867-4.1710.215270.1943730.196400100
4.171-4.560.191230.1863440.187367100
4.56-5.0840.345120.2223320.226344100
5.084-5.8420.347100.2512880.254298100
5.842-7.0880.304280.2812350.284263100
7.088-9.7560.19450.2092150.208220100
9.756-300.251110.2191320.22114995.973

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