PDB-5yz5: Crystal Structure of Human CRMP-2 with T509D-T514D-S518D-S522D mu...

ID or keywords:

Entry

Database: PDB / ID: 5yz5

Title

Crystal Structure of Human CRMP-2 with T509D-T514D-S518D-S522D mutations

Components

Dihydropyrimidinase-related protein 2

Keywords

CYTOSOLIC PROTEIN / developmental protein / phosphoprotein / microtubule associated proteins / neurogenesis / dihydropyrimidase-related protein / collapsin response mediator protein / protein binding

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.8 Å

Authors

Imasaki, T. / Sumi, T. / Aoki, M. / Sakai, N. / Nitta, E. / Shirouzu, M. / Nitta, R.

Funding support

Japan, 3items

Citation

Journal: Cell Struct. Funct. / Year: 2018
Title: Structural Insights into the Altering Function of CRMP2 by Phosphorylation.
Authors: Sumi, T. / Imasaki, T. / Aoki, M. / Sakai, N. / Nitta, E. / Shirouzu, M. / Nitta, R.

History

Deposition	Dec 13, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5yz5.cif.gz	116.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5yz5.ent.gz	88.8 KB	Display	PDB format
PDBx/mmJSON format	5yz5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5yz5_validation.pdf.gz	438.6 KB	Display	wwPDB validaton report
Full document	5yz5_full_validation.pdf.gz	441.2 KB	Display
Data in XML	5yz5_validation.xml.gz	22.2 KB	Display
Data in CIF	5yz5_validation.cif.gz	33.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yz/5yz5 ftp://data.pdbj.org/pub/pdb/validation_reports/yz/5yz5	HTTPS FTP

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Related structure data

Related structure data	5yzaC 5yzbC 5x1a 5x1c 5x1d C: citing same article (ref.)
Similar structure data	5yzb-1 6ajd-d 4h00-2 4h01-2 4gz7-2 7kzi-1 1lvc-2 6zrd-d 6dzv-d 1va6-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (4) #158 - Feb 2013 Proton-Gated Urea Channel similarity (4) #88 - Apr 2007 Clathrin similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: Dihydropyrimidinase-related protein 2

hetero molecules

57.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Dihydropyrimidinase-related protein 2

hetero molecules

A: Dihydropyrimidinase-related protein 2

hetero molecules

defined by software
Evidence: SAXS
115 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	114.117, 114.117, 196.074
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-918- HOH
2	1	A-920- HOH
3	1	A-927- HOH
4	1	A-956- HOH
5	1	A-990- HOH
6	1	A-1047- HOH

#1: Protein	Dihydropyrimidinase-related protein 2 / DRP-2 / Collapsin response mediator protein 2 / CRMP-2 / N2A3 / Unc-33-like phosphoprotein 2 / ULIP-2 Mass: 57467.832 Da / Num. of mol.: 1 / Mutation: T509D/T514D/S518D/S522D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPYSL2, CRMP2, ULIP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q16555
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.78 Å³/Da / Density % sol: 55.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 12% PEG 4000, 0.1M sodium citrate pH 5.6, 0.1M lithium sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 12, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 114502 / % possible obs: 99.8 % / Redundancy: 7.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.055 / R_rim(I) all: 0.059 / Net I/σ(I): 19.8
Reflection shell	Resolution: 1.8→1.91 Å / Redundancy: 7.4 % / R_merge(I) obs: 1.116 / Mean I/σ(I) obs: 1.89 / R_rim(I) all: 1.199 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Resolution: 1.8→40.224 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.55
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS

	R_factor	Num. reflection	% reflection
R_free	0.219	3795	3.31 %
R_work	0.1863	-	-
obs	0.1874	114502	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.8→40.224 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3785	0	5	352	4142

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3901
X-RAY DIFFRACTION	f_angle_d	0.829	5297
X-RAY DIFFRACTION	f_dihedral_angle_d	19.321	1434
X-RAY DIFFRACTION	f_chiral_restr	0.053	593
X-RAY DIFFRACTION	f_plane_restr	0.005	693

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7997-1.8225	0.3089	141	0.3032	4073	X-RAY DIFFRACTION	99
1.8225-1.8465	0.2987	143	0.2889	4113	X-RAY DIFFRACTION	100
1.8465-1.8718	0.3071	138	0.2757	4106	X-RAY DIFFRACTION	100
1.8718-1.8985	0.3712	143	0.2658	4091	X-RAY DIFFRACTION	100
1.8985-1.9268	0.3959	135	0.3769	4079	X-RAY DIFFRACTION	99
1.9268-1.9569	0.2849	140	0.2677	4100	X-RAY DIFFRACTION	100
1.9569-1.989	0.3153	140	0.2538	4092	X-RAY DIFFRACTION	100
1.989-2.0233	0.2821	141	0.2446	4092	X-RAY DIFFRACTION	100
2.0233-2.0601	0.304	139	0.2326	4090	X-RAY DIFFRACTION	100
2.0601-2.0997	0.2685	141	0.2256	4110	X-RAY DIFFRACTION	100
2.0997-2.1426	0.2752	141	0.2149	4124	X-RAY DIFFRACTION	100
2.1426-2.1892	0.2469	142	0.2221	4105	X-RAY DIFFRACTION	100
2.1892-2.2401	0.2736	137	0.2314	4089	X-RAY DIFFRACTION	100
2.2401-2.2961	0.2411	141	0.2587	4074	X-RAY DIFFRACTION	100
2.2961-2.3582	0.2459	142	0.2014	4117	X-RAY DIFFRACTION	100
2.3582-2.4276	0.2272	139	0.2021	4098	X-RAY DIFFRACTION	100
2.4276-2.5059	0.2366	137	0.195	4079	X-RAY DIFFRACTION	100
2.5059-2.5955	0.2176	145	0.1991	4152	X-RAY DIFFRACTION	100
2.5955-2.6994	0.2199	142	0.1833	4102	X-RAY DIFFRACTION	100
2.6994-2.8222	0.202	138	0.1912	4109	X-RAY DIFFRACTION	100
2.8222-2.9709	0.2814	138	0.1865	4079	X-RAY DIFFRACTION	100
2.9709-3.157	0.2356	141	0.1905	4110	X-RAY DIFFRACTION	100
3.157-3.4006	0.2247	144	0.1893	4094	X-RAY DIFFRACTION	100
3.4006-3.7426	0.2205	143	0.1712	4126	X-RAY DIFFRACTION	100
3.7426-4.2837	0.1634	141	0.1444	4098	X-RAY DIFFRACTION	100
4.2837-5.3949	0.1659	141	0.1399	4105	X-RAY DIFFRACTION	100
5.3949-40.2344	0.1699	142	0.152	4100	X-RAY DIFFRACTION	100

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