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- PDB-2b0o: Crystal structure of UPLC1 GAP domain -

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Basic information

Entry
Database: PDB / ID: 2b0o
TitleCrystal structure of UPLC1 GAP domain
ComponentsUPLC1
KeywordsMETAL BINDING PROTEIN / ARFGAP / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of stress fiber assembly / ruffle / GTPase activator activity / positive regulation of GTPase activity / cell migration / focal adhesion / intracellular membrane-bounded organelle / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Arf GTPase activating protein, ASAP3 / : / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / Arf GTPase activating protein / BAR domain of APPL family / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. ...Arf GTPase activating protein, ASAP3 / : / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / Arf GTPase activating protein / BAR domain of APPL family / 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 / BAR domain / ARFGAP/RecO-like zinc finger / Domain of unknown function DUF3447 / Annexin V; domain 1 / AH/BAR domain superfamily / Ankyrin repeat-containing domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsIsmail, S. / Shen, L. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structural analysis of GAP and ankyrin domains of UPLC1
Authors: Ismail, S. / Shen, L. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionSep 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: UPLC1
F: UPLC1
G: UPLC1
H: UPLC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,4028
Polymers131,1404
Non-polymers2624
Water9,008500
1
E: UPLC1
F: UPLC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7014
Polymers65,5702
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-20 kcal/mol
Surface area22430 Å2
MethodPISA
2
G: UPLC1
H: UPLC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7014
Polymers65,5702
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-14 kcal/mol
Surface area21690 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-47 kcal/mol
Surface area42120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.055, 106.716, 100.365
Angle α, β, γ (deg.)90.00, 98.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
UPLC1


Mass: 32785.074 Da / Num. of mol.: 4 / Fragment: GAP domain (residues 414-697)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDEFL1 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6P9F4, UniProt: Q8TDY4*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: NaCitrat 1.5M, Ethylene Glycol 9%, Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.059→50 Å / Num. all: 67919 / Num. obs: 67919 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rsym value: 0.063 / Net I/σ(I): 17.2
Reflection shellResolution: 2.059→2.13 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 6157 / Rsym value: 0.27 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DCQ

1dcq


Resolution: 2.06→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.307 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.203 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23264 3414 5 %RANDOM
Rwork0.1826 ---
obs0.18518 64496 97.57 %-
all-66102 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.234 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0.15 Å2
2---0.3 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.06→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7988 0 4 500 8492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0218132
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.9711013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35551034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15524.56364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.669151379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9111552
X-RAY DIFFRACTIONr_chiral_restr0.1360.21253
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026130
X-RAY DIFFRACTIONr_nbd_refined0.2280.24130
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25501
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2563
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.213
X-RAY DIFFRACTIONr_mcbond_it1.2141.55394
X-RAY DIFFRACTIONr_mcangle_it1.85128265
X-RAY DIFFRACTIONr_scbond_it3.04533118
X-RAY DIFFRACTIONr_scangle_it4.6724.52748
LS refinement shellResolution: 2.059→2.112 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 215 -
Rwork0.201 4166 -
obs--86.65 %

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