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- PDB-5uqc: Crystal structure of mouse CRMP2 -

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Basic information

Entry
Database: PDB / ID: 5uqc
TitleCrystal structure of mouse CRMP2
ComponentsDihydropyrimidinase-related protein 2
KeywordsSIGNALING PROTEIN / SUMOylation / TRANSCRIPTION
Function / homology
Function and homology information


CRMPs in Sema3A signaling / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / Recycling pathway of L1 / positive regulation of glutamate secretion / regulation of neuron differentiation / synaptic vesicle transport / regulation of neuron projection development / cytoskeleton organization / Schaffer collateral - CA1 synapse / endocytosis ...CRMPs in Sema3A signaling / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / Recycling pathway of L1 / positive regulation of glutamate secretion / regulation of neuron differentiation / synaptic vesicle transport / regulation of neuron projection development / cytoskeleton organization / Schaffer collateral - CA1 synapse / endocytosis / myelin sheath / presynapse / nervous system development / growth cone / postsynaptic density / cell differentiation / cytoskeleton / axon / neuronal cell body / dendrite / synapse / protein kinase binding / protein-containing complex / mitochondrion / membrane / cytosol
Similarity search - Function
Hydantoinase/dihydropyrimidinase / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll ...Hydantoinase/dihydropyrimidinase / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-1PG / Dihydropyrimidinase-related protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsKhanna, M. / Khanna, R. / Perez-Miller, S. / Francois-Moutal, L.
CitationJournal: Channels (Austin) / Year: 2017
Title: A single structurally conserved SUMOylation site in CRMP2 controls NaV1.7 function.
Authors: Dustrude, E.T. / Perez-Miller, S. / Francois-Moutal, L. / Moutal, A. / Khanna, M. / Khanna, R.
History
DepositionFeb 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydropyrimidinase-related protein 2
B: Dihydropyrimidinase-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0203
Polymers105,7672
Non-polymers2521
Water16,808933
1
A: Dihydropyrimidinase-related protein 2
B: Dihydropyrimidinase-related protein 2
hetero molecules

A: Dihydropyrimidinase-related protein 2
B: Dihydropyrimidinase-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,0396
Polymers211,5354
Non-polymers5052
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area12550 Å2
ΔGint-7 kcal/mol
Surface area60680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.412, 107.222, 81.680
Angle α, β, γ (deg.)90.000, 120.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dihydropyrimidinase-related protein 2 / DRP-2 / Unc-33-like phosphoprotein 2 / ULIP-2


Mass: 52883.629 Da / Num. of mol.: 2 / Fragment: residues 15-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dpysl2, Crmp2, Ulip2 / Production host: Escherichia coli (E. coli) / References: UniProt: O08553
#2: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 933 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M Bis-Tris pH 6, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.78→39.22 Å / Num. obs: 552156 / % possible obs: 99.94 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Net I/σ(I): 23.1
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.539 / % possible all: 82.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.459
Highest resolutionLowest resolution
Rotation39.18 Å1.8 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.7data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSE

2gse


Resolution: 1.78→35 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.141 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.173 4698 5 %RANDOM
Rwork0.135 ---
obs0.137 89737 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.38 Å2 / Biso mean: 23.91 Å2 / Biso min: 10.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20.22 Å2
2---0.52 Å20 Å2
3---0.78 Å2
Refinement stepCycle: final / Resolution: 1.78→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7406 0 17 964 8387
Biso mean--40.03 35.47 -
Num. residues----961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197672
X-RAY DIFFRACTIONr_bond_other_d0.0030.027300
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.94910401
X-RAY DIFFRACTIONr_angle_other_deg1.124316855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9325960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96324.699349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.135151318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.261544
X-RAY DIFFRACTIONr_chiral_restr0.1170.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218663
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021687
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 349 -
Rwork0.202 6564 -
all-6913 -
obs--99.8 %

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