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- PDB-3qwe: Crystal structure of the N-terminal domain of the GEM interacting... -

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Basic information

Entry
Database: PDB / ID: 3qwe
TitleCrystal structure of the N-terminal domain of the GEM interacting protein
ComponentsGEM-interacting protein
KeywordsPROTEIN BINDING / structural genomics consortium / SGC
Function / homology
Function and homology information


: / activation of GTPase activity / regulation of small GTPase mediated signal transduction / negative regulation of GTPase activity / GTPase activator activity / intracellular signal transduction / nucleoplasm / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Arfaptin homology (AH) domain/BAR domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Rho GTPase activation protein ...Arfaptin homology (AH) domain/BAR domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Rho GTPase activation protein / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
GEM-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsGuan, X. / Tempel, W. / Tong, Y. / Shen, L. / Wang, H. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Guan, X. / Tempel, W. / Tong, Y. / Shen, L. / Wang, H. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the N-terminal domain of the GEM interacting protein
Authors: Guan, X. / Tempel, W. / Tong, Y. / Shen, L. / Wang, H. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GEM-interacting protein


Theoretical massNumber of molelcules
Total (without water)32,18430
Polymers32,1841
Non-polymers029
Water00
1
A: GEM-interacting protein

A: GEM-interacting protein


Theoretical massNumber of molelcules
Total (without water)64,36760
Polymers64,3672
Non-polymers058
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area6830 Å2
ΔGint-67 kcal/mol
Surface area27780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.530, 57.530, 500.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsBIOLOGICAL ASSEMBLY IS UNKNOWN AS PER AUTHORS

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Components

#1: Protein GEM-interacting protein / GMIP


Mass: 32183.525 Da / Num. of mol.: 1 / Fragment: UNP residues 80-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GMIP / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9P107
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 29 / Source method: obtained synthetically

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
1468.6
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG-1500, 0.2M sodium chloride, 0.1M HEPES, 5% ethylene glycol, 3% glucose monohydrate. Crystals were de-hydrated by addition of 5% glycerol to reservoir solution, incubation over-night, ...Details: 20% PEG-1500, 0.2M sodium chloride, 0.1M HEPES, 5% ethylene glycol, 3% glucose monohydrate. Crystals were de-hydrated by addition of 5% glycerol to reservoir solution, incubation over-night, pH 7.5, vapor diffusion, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCLSI 08ID-110.92017
SYNCHROTRONAPS 19-ID20.97911
Detector
TypeIDDetectorDate
RAYONIX MX-3001CCDJan 21, 2011
ADSC QUANTUM 3152CCDDec 18, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.920171
20.979111
ReflectionResolution: 2.4→50 Å / Num. obs: 20751 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 68.077 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.19
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.460.9452.221132144599.9
2.46-2.530.6883216171449100
2.53-2.60.574219531409100
2.6-2.680.4974.8222271354100
2.68-2.770.3996.4229081353100
2.77-2.870.2839.1232231306100
2.87-2.980.21612.4226831229100
2.98-3.10.15916.723016121299.9
3.1-3.240.12223.2223381175100
3.24-3.390.10628.2214141119100
3.39-3.580.08834.3203361077100
3.58-3.790.06841.8187081000100
3.79-4.060.06246.717820971100
4.06-4.380.05449.216582904100
4.38-4.80.04852.115669866100
4.8-5.370.04552.813989750100
5.37-6.20.04750.913021712100
6.2-7.590.03954.510996611100
7.59-10.730.03157822949499.4
10.73-300.02951.6422931596.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
DENZOdata reduction
XSCALEdata scaling
SCALEPACKdata scaling
SHELXDEphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.9215 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
Details: PROGRAMS BUCCANEER, PHENIX, REFMAC, COOT AND THE MOLPROBITY SERVER WERE ALSO USED DURING REFINEMENT. FOR THIS STRUCTURE, CROSS-VALIDATION IS SUBJECT TO LARGE VARIATIONS IN RFREE, DEPENDING ...Details: PROGRAMS BUCCANEER, PHENIX, REFMAC, COOT AND THE MOLPROBITY SERVER WERE ALSO USED DURING REFINEMENT. FOR THIS STRUCTURE, CROSS-VALIDATION IS SUBJECT TO LARGE VARIATIONS IN RFREE, DEPENDING ON THE SELECTED FREE SET. THE CURRENT SET OF FREE REFLECTIONS PRODUCES AN UNREASONABLY LOW RFREE. THIS WAS CONFIRMED BY A MULTI-STEP REFINEMENT RUN THAT USED AN ALTERNATIVE SUBSET OF REFLECTIONS FOR CALCULATION OF RFREE. WE COULD NOT CONFIDENTLY INTERPRET DIFFERENCE DENSITY AT THE CURRENT MODEL'S C-TERMINUS. AMINO ACID SEQUENCE ALIGNMENT TO THE MODEL LARGELY RELIED ON THE SELENOMETHIONINE POSITIONS OBTAINED DURING PHASING. ONLY MODERATE MAP QUALITY COMBINED WITH GAPS IN THE DENSITY GIVES RISE TO SOME UNCERTAINTY IN THE AMINO ACID SEQUENCE ALIGNMENT IN SOME PARTS OF THE MODEL. DIFFRACTION IMAGES SHOW ANISOTROPIC HIGH RESOLUTION LIMITS. THE ELECTRON DENSITY MAP USED FOR MODEL BUILDING APPEARED TO BE OF SIGNIFICANTLY LOWER QUALITY THAN THE QUOTED HIGHER RESOLUTION LIMITS SUGGEST. WATER MOLECULES WERE NOT EXPLICITLY MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 1020 4.92 %RANDOM
Rwork0.2265 ---
obs0.2267 20742 --
Displacement parametersBiso max: 148.37 Å2 / Biso mean: 74.5335 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--10.703 Å20 Å20 Å2
2---10.703 Å20 Å2
3---21.406 Å2
Refine analyzeLuzzati coordinate error obs: 0.462 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 29 0 2047
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d7322
X-RAY DIFFRACTIONt_trig_c_planes492
X-RAY DIFFRACTIONt_gen_planes3075
X-RAY DIFFRACTIONt_it205020
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2645
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact23254
X-RAY DIFFRACTIONt_bond_d205020.01
X-RAY DIFFRACTIONt_angle_deg276320.98
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion18.32
LS refinement shellResolution: 2.4→2.53 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2901 148 5.12 %
Rwork0.2448 2743 -
all0.2471 2891 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.18560.0463-1.09470.4004-0.19421.41660.0035-0.055-0.06720.0241-0.01-0.0252-0.0047-0.03220.00650.121-0.00420.06080.27940.1986-0.239727.7619-1.024886.9533
20.4935-0.1131-0.2719-0.2951-0.05932.3327-0.1329-0.05930.02840.09350.0453-0.0270.01220.23320.08760.0626-0.10330.0206-0.07350.1873-0.006844.92967.104953.0139
30.0156-0.2790.36180.9302-2.86176.6751-0.1051-0.14350.05940.0769-0.2023-0.1646-0.3670.41650.30740.0775-0.2007-0.01370.14760.1676-0.063745.44722.126874.1387
40.3393-0.21070.2703-0.2879-0.64262.7873-0.1389-0.25220.03320.1320.1073-0.0434-0.43950.06970.03160.1945-0.0778-0.07930.05290.0549-0.085439.64260.960585.7061
5-0.8671-0.1358-1.23743.07180.36561.27230.0461-0.0020.1076-0.033-0.131-0.0277-0.0442-0.11090.0850.2110.03890.0055-0.00780.1099-0.239941.335425.87258.8544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|80 - 90}A80 - 90
2X-RAY DIFFRACTION2{A|91 - 143}A91 - 143
3X-RAY DIFFRACTION3{A|144 - 233}A144 - 233
4X-RAY DIFFRACTION4{A|247 - 338}A247 - 338
5X-RAY DIFFRACTION5{A|339 - 352}A339 - 352

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