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- PDB-6jv9: Crystal Structure of Human CRMP2 1-532, unmodified -

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Basic information

Entry
Database: PDB / ID: 6jv9
TitleCrystal Structure of Human CRMP2 1-532, unmodified
ComponentsDihydropyrimidinase-related protein 2
KeywordsSTRUCTURAL PROTEIN / Microtubule associated protein / GAP activity / Neuronal protein
Function / homology
Function and homology information


dihydropyrimidinase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / CRMPs in Sema3A signaling / nucleobase-containing compound metabolic process / Recycling pathway of L1 / cytoskeleton organization / endocytosis / nervous system development / cell differentiation / cytoskeleton ...dihydropyrimidinase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / CRMPs in Sema3A signaling / nucleobase-containing compound metabolic process / Recycling pathway of L1 / cytoskeleton organization / endocytosis / nervous system development / cell differentiation / cytoskeleton / signal transduction / extracellular exosome / identical protein binding / plasma 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 / TIM Barrel ...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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / TRIETHYLENE GLYCOL / Dihydropyrimidinase-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsJiang, X. / Ogawa, T. / Hirokawa, N.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18dm0908001 Japan
Japan Agency for Medical Research and Development (AMED)JP18dm0107083 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101070 Japan
CitationJournal: Life Sci Alliance / Year: 2019
Title: Enhanced carbonyl stress induces irreversible multimerization of CRMP2 in schizophrenia pathogenesis.
Authors: Toyoshima, M. / Jiang, X. / Ogawa, T. / Ohnishi, T. / Yoshihara, S. / Balan, S. / Yoshikawa, T. / Hirokawa, N.
History
DepositionApr 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)237,5999
Polymers237,0404
Non-polymers5595
Water10,287571
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-71 kcal/mol
Surface area62550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.088, 158.425, 88.000
Angle α, β, γ (deg.)90.00, 94.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPTYRTYRAA15 - 49923 - 507
21ASPASPTYRTYRBB15 - 49923 - 507
12ASPASPARGARGAA15 - 49623 - 504
22ASPASPARGARGCC15 - 49623 - 504
13ASPASPPROPROAA15 - 49523 - 503
23ASPASPPROPRODD15 - 49523 - 503
14ASPASPARGARGBB15 - 49623 - 504
24ASPASPARGARGCC15 - 49623 - 504
15SERSERPROPROBB14 - 49522 - 503
25SERSERPROPRODD14 - 49522 - 503
16ASPASPPROPROCC15 - 49523 - 503
26ASPASPPROPRODD15 - 49523 - 503

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dihydropyrimidinase-related protein 2 / DRP-2 / Collapsin response mediator protein 2 / CRMP-2 / N2A3 / Unc-33-like phosphoprotein 2 / ULIP-2


Mass: 59259.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPYSL2, CRMP2, ULIP2 / Production host: Escherichia coli (E. coli) / Strain (production host): K19 / References: UniProt: Q16555

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Non-polymers , 5 types, 576 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES (pH 6.0), 15% (v/v) PEG 400, 0.1 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 102278 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.106 / Net I/σ(I): 6.5
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5113 / CC1/2: 0.64 / Rpim(I) all: 0.375 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MKV

5mkv


Resolution: 2.26→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.552 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.177 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19337 5112 5 %RANDOM
Rwork0.17066 ---
obs0.17181 97166 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.953 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.19 Å2
2---0.83 Å2-0 Å2
3---1.43 Å2
Refinement stepCycle: 1 / Resolution: 2.26→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14883 0 32 571 15486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01915219
X-RAY DIFFRACTIONr_bond_other_d0.0060.0214376
X-RAY DIFFRACTIONr_angle_refined_deg1.521.9520646
X-RAY DIFFRACTIONr_angle_other_deg1.849333136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79851943
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33424.612657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.734152522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8931580
X-RAY DIFFRACTIONr_chiral_restr0.0820.22336
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117308
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023348
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_it2.0722.9177784
X-RAY DIFFRACTIONr_mcbond_other2.0722.9167783
X-RAY DIFFRACTIONr_mcangle_it3.1274.3659723
X-RAY DIFFRACTIONr_mcangle_other3.1274.3659724
X-RAY DIFFRACTIONr_scbond_it3.033.2567435
X-RAY DIFFRACTIONr_scbond_other3.0213.2537431
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7224.72810918
X-RAY DIFFRACTIONr_long_range_B_refined6.01423.03816529
X-RAY DIFFRACTIONr_long_range_B_other6.00922.98716387
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A606920.05
12B606920.05
21A607380.04
22C607380.04
31A603600.05
32D603600.05
41B607860.03
42C607860.03
51B605100.05
52D605100.05
61C606660.04
62D606660.04
LS refinement shellResolution: 2.257→2.315 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 349 -
Rwork0.221 7053 -
obs--98.03 %

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