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- PDB-2iqj: Crystal structure of the GAP domain of SMAP1L (LOC64744) stromal ... -

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Basic information

Entry
Database: PDB / ID: 2iqj
TitleCrystal structure of the GAP domain of SMAP1L (LOC64744) stromal membrane-associated protein 1-like
ComponentsStromal membrane-associated protein 1-like
KeywordsPROTEIN TRANSPORT / zinc / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / stromal / membrane-associated
Function / homology
Function and homology information


GTPase activator activity / metal ion binding / cytoplasm
Similarity search - Function
Arf GTPase activating protein / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Stromal membrane-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsTong, Y. / Dimov, S. / Shen, L. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. ...Tong, Y. / Dimov, S. / Shen, L. / 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: Structure of the GAP domain of SMAP1L (LOC64744) stromal membrane-associated protein 1-like
Authors: Tong, Y. / Dimov, S. / Shen, L. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionOct 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 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
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 / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 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: Stromal membrane-associated protein 1-like
B: Stromal membrane-associated protein 1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1929
Polymers30,9052
Non-polymers2877
Water1,17165
1
A: Stromal membrane-associated protein 1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5964
Polymers15,4531
Non-polymers1443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Stromal membrane-associated protein 1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5965
Polymers15,4531
Non-polymers1444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.812, 38.513, 47.386
Angle α, β, γ (deg.)90.10, 108.89, 105.13
Int Tables number1
Space group name H-MP1
Detailsnot known

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Components

#1: Protein Stromal membrane-associated protein 1-like


Mass: 15452.660 Da / Num. of mol.: 2 / Fragment: GAP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMAP1L / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE-3)-RIL / References: UniProt: Q8WU79
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


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


Num. of mol.: 3 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.1 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG-3350, 0.2M Ammonium acetate, 0.1M Bis-Tris, 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: Sep 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 17983 / % possible obs: 94.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.052 / Χ2: 1.603 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
1.85-1.9290.53.90.38117311.255
1.92-1.9991.23.90.29417101.364
1.99-2.0891.83.90.22217661.451
2.08-2.1992.73.90.15417831.614
2.19-2.3393.63.90.12318061.725
2.33-2.5194.53.90.09317941.706
2.51-2.7694.93.90.07218081.738
2.76-3.1696.240.05118431.741
3.16-3.9897.13.90.03518521.788
3.98-2098.63.90.02918901.595

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å19.96 Å
Translation2.5 Å19.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CRR

2crr


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.185 / SU B: 3.872 / SU ML: 0.117 / Cross valid method: FREE R / ESU R: 0.195 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Arp/warp, molprobity, coot have also been used in structure solution and refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 998 5.995 %thin shells
Rwork0.1915 ---
obs0.195 16648 94.334 %-
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: 20.834 Å2
Baniso -1Baniso -2Baniso -3
1-0.336 Å2-0.612 Å20.204 Å2
2--0.198 Å2-0.296 Å2
3----0.722 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 11 65 2017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221998
X-RAY DIFFRACTIONr_bond_other_d0.0020.021386
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9422693
X-RAY DIFFRACTIONr_angle_other_deg0.9563.0063347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23824.314102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66515349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6661515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02412
X-RAY DIFFRACTIONr_nbd_refined0.1980.2381
X-RAY DIFFRACTIONr_nbd_other0.1890.21482
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2958
X-RAY DIFFRACTIONr_nbtor_other0.0840.2979
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.25
X-RAY DIFFRACTIONr_mcbond_it2.71721359
X-RAY DIFFRACTIONr_mcbond_other0.7972491
X-RAY DIFFRACTIONr_mcangle_it3.20631933
X-RAY DIFFRACTIONr_scbond_it2.4712885
X-RAY DIFFRACTIONr_scangle_it3.5273757
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 (%)
1.9-1.9490.367620.24911420.256133190.458
1.949-2.0020.322780.21710620.224124191.861
2.002-2.060.3361020.2210320.23123491.896
2.06-2.12300.20711000.207119791.896
2.123-2.1920.2721020.1979830.205116992.814
2.192-2.26900.20910530.209112193.934
2.269-2.3540.2741070.2049160.211109493.51
2.354-2.450.258920.1928870.198104393.864
2.45-2.55800.1879360.18798794.833
2.558-2.6820.251810.2038450.20797295.267
2.682-2.8250.262760.1977880.20390595.47
2.825-2.99500.2168200.21685595.906
2.995-3.20.258620.2027420.20683296.635
3.2-3.4530.26500.1866650.19173896.883
3.453-3.7770.212430.1726330.17469397.547
3.777-4.2150.186400.1585630.1661897.573
4.215-4.8510.175280.1455300.14756898.239
4.851-5.9030.224400.1924250.19547298.517
5.903-8.1910.235200.213370.21236099.167
8.191-300.222150.2011910.20321894.495

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