[English] 日本語
Yorodumi
- PDB-2gse: Crystal Structure of Human Dihydropyrimidinease-like 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gse
TitleCrystal Structure of Human Dihydropyrimidinease-like 2
ComponentsDihydropyrimidinase-related protein 2
KeywordsHYDROLASE / alpha/beta barrel / Structural Genomics / Structural Genomics Consortium / SGC / Dihydropyrimidinase-Related Protein 2 / DRP2 / Collapsin Response Mediator Protein 2 / CRMP2
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
Dihydropyrimidinase-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOgg, D. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. ...Ogg, D. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hallberg, B.M. / Hammarstrom, M. / Kotenyova, T. / Kursula, P. / Nilsson-Ehle, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Holmberg-Schiavone, L. / Thorsell, A.G. / Uppenberg, J. / Van Den Berg, S. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: J.Neurochem. / Year: 2007
Title: The structure of human collapsin response mediator protein 2, a regulator of axonal growth.
Authors: Stenmark, P. / Ogg, D. / Flodin, S. / Flores, A. / Kotenyova, T. / Nyman, T. / Nordlund, P. / Kursula, P.
History
DepositionApr 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Feb 14, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)220,5488
Polymers220,3884
Non-polymers1604
Water15,295849
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-54 kcal/mol
Surface area60220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.400, 126.100, 102.900
Angle α, β, γ (deg.)90.00, 113.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 6 / Auth seq-ID: 17 - 485 / Label seq-ID: 28 - 496

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe biological assemby is a tetramer

-
Components

#1: Protein
Dihydropyrimidinase-related protein 2 / DRP-2 / Collapsin response mediator protein 2 / CRMP-2 / N2A3


Mass: 55096.969 Da / Num. of mol.: 4 / Fragment: Dihydropyrimidinase-like 2 (13-490)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPYSL2 / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q16555, dihydropyrimidinase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 849 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18% PEG 10k, 0.1M Tris, 0.2M CaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2006 / Details: MIRRORS
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 79391 / Num. obs: 79142 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 9.6
Reflection shellResolution: 2.4→2.6 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.36 / Num. unique all: 16757 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ProDCdata collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.31 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.882 / SU B: 8.776 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.448 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3960 5 %RANDOM
Rwork0.169 ---
obs0.173 75230 99.96 %-
all-79190 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.36 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.02 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14638 0 4 849 15491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02214938
X-RAY DIFFRACTIONr_bond_other_d0.0010.029970
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9520270
X-RAY DIFFRACTIONr_angle_other_deg0.98324423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57251897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66224.764657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.135152526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8921576
X-RAY DIFFRACTIONr_chiral_restr0.0890.22289
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216731
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022885
X-RAY DIFFRACTIONr_nbd_refined0.2070.23178
X-RAY DIFFRACTIONr_nbd_other0.1980.210593
X-RAY DIFFRACTIONr_nbtor_refined0.1760.27148
X-RAY DIFFRACTIONr_nbtor_other0.0880.27846
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2913
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0120.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1670.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.25
X-RAY DIFFRACTIONr_mcbond_it0.6961.59790
X-RAY DIFFRACTIONr_mcbond_other0.1281.53866
X-RAY DIFFRACTIONr_mcangle_it1.153215258
X-RAY DIFFRACTIONr_scbond_it1.69735966
X-RAY DIFFRACTIONr_scangle_it2.5864.55012
Refine LS restraints NCS

Ens-ID: 1 / Number: 6059 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.35
2Bloose positional0.315
3Cloose positional0.315
4Dloose positional0.35
1Aloose thermal1.7210
2Bloose thermal1.6510
3Cloose thermal1.7310
4Dloose thermal1.7210
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 291 -
Rwork0.216 5519 -
obs--100 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more