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- PDB-4gn1: Crystal Structure of the RA and PH domains of Lamellipodin -

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Basic information

Entry
Database: PDB / ID: 4gn1
TitleCrystal Structure of the RA and PH domains of Lamellipodin
ComponentsRas-associated and pleckstrin homology domains-containing protein 1
KeywordsSIGNALING PROTEIN / RA-PH / coiled-coil region / Ras-association domain / pleckstrin homology domain / cytoskeletal protein / Ena/VASP binding / cell migration / cell adhesion
Function / homology
Function and homology information


axon extension / filopodium / lamellipodium / cytoskeleton / nuclear body / signal transduction / plasma membrane / cytosol
Similarity search - Function
GRB/APBB1IP / APBB1IP, PH domain / RA like domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain ...GRB/APBB1IP / APBB1IP, PH domain / RA like domain / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ubiquitin-like (UB roll) / PH-like domain superfamily / Roll / Ubiquitin-like domain superfamily / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Ras-associated and pleckstrin homology domains-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChang, Y.C.E. / Wu, J.
CitationJournal: Protein Cell / Year: 2013
Title: Crystal structure of Lamellipodin implicates diverse functions in actin polymerization and Ras signaling.
Authors: Chang, Y.C. / Zhang, H. / Brennan, M.L. / Wu, J.
History
DepositionAug 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Ras-associated and pleckstrin homology domains-containing protein 1
B: Ras-associated and pleckstrin homology domains-containing protein 1
C: Ras-associated and pleckstrin homology domains-containing protein 1
D: Ras-associated and pleckstrin homology domains-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4208
Polymers121,0124
Non-polymers4084
Water4,486249
1
A: Ras-associated and pleckstrin homology domains-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3552
Polymers30,2531
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras-associated and pleckstrin homology domains-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3552
Polymers30,2531
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ras-associated and pleckstrin homology domains-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3552
Polymers30,2531
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ras-associated and pleckstrin homology domains-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3552
Polymers30,2531
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.340, 93.465, 80.720
Angle α, β, γ (deg.)90.00, 104.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ras-associated and pleckstrin homology domains-containing protein 1 / RAPH1 / Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 18 protein / Amyotrophic ...RAPH1 / Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 18 protein / Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 9 protein / Lamellipodin / Proline-rich EVH1 ligand 2 / PREL-2 / Protein RMO1


Mass: 30252.963 Da / Num. of mol.: 4 / Fragment: RA and PH domain (UNP Residues 266-520)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAPH1, ALS2CR18, ALS2CR9, KIAA1681, LPD, PREL2, RMO1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q70E73
#2: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM sodium malonate pH 5.0, 20% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2012
RadiationMonochromator: Si-111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→46.73 Å / Num. obs: 41656 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 2.4→2.44 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
ARP/wARPmodel building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TCA

3tca


Resolution: 2.4→46.73 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 21.607 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.746 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.303 2158 5.1 %RANDOM
Rwork0.253 ---
all0.314 ---
obs0.256 39803 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.836 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.05 Å2
2--0.16 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8173 0 28 249 8450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.028400
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.96111313
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65924.423416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.478151636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0571550
X-RAY DIFFRACTIONr_chiral_restr0.0970.21214
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026254
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 164 -
Rwork0.312 2870 -
obs--99.15 %
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)
11.67750.25730.15021.97310.16071.5979-0.11520.23460.2705-0.03090.082-0.1206-0.17730.25120.03320.0533-0.033-0.0270.06860.03470.065717.4221-0.51721.1992
22.08550.27920.39111.94390.2011.8119-0.12830.35880.1143-0.03840.1328-0.1527-0.19430.3272-0.00450.0888-0.0126-0.02220.12230.00240.035649.7053-0.497240.8233
32.22290.52960.48552.00330.39811.85060.05710.47050.0874-0.02560.097-0.11240.02390.3727-0.1540.04610.04670.00020.1668-0.0020.053227.0036-0.1958-16.895
42.60260.10370.68612.33810.16781.7729-0.15770.53940.3985-0.02590.003-0.0765-0.22770.41340.15470.0621-0.0634-0.04970.15880.09220.079559.562-0.20172.6752
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A268 - 518
2X-RAY DIFFRACTION2B268 - 517
3X-RAY DIFFRACTION3C268 - 517
4X-RAY DIFFRACTION4D268 - 517

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