[English] 日本語
Yorodumi
- PDB-4b91: Crystal structure of truncated human CRMP-5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b91
TitleCrystal structure of truncated human CRMP-5
ComponentsDIHYDROPYRIMIDINASE-RELATED PROTEIN 5
KeywordsSIGNALING PROTEIN / NEUROGENESIS / PHOSPHOPROTEIN / CRMP / TIM BARREL / AXONAL OUTGROWTH / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / negative regulation of dendrite morphogenesis / CRMPs in Sema3A signaling / axon guidance / nervous system development / dendrite / neuronal cell body / signal transduction / protein-containing complex / cytosol
Similarity search - Function
Hydantoinase/dihydropyrimidinase / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Dihydropyrimidinase-related protein 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPonnusamy, R. / Lohkamp, B.
CitationJournal: J.Neurochem. / Year: 2013
Title: Insights Into the Oligomerization of Crmps: Crystal Structure of Human Collapsin Response Mediator Protein 5.
Authors: Ponnusamy, R. / Lohkamp, B.
History
DepositionAug 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5


Theoretical massNumber of molelcules
Total (without water)105,9072
Polymers105,9072
Non-polymers00
Water10,485582
1
A: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5

A: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5


Theoretical massNumber of molelcules
Total (without water)211,8144
Polymers211,8144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area8850 Å2
ΔGint-27.6 kcal/mol
Surface area62380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.090, 90.090, 248.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 8 - 480 / Label seq-ID: 9 - 481

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given)

-
Components

#1: Protein DIHYDROPYRIMIDINASE-RELATED PROTEIN 5 / DRP-5 / CRMP3-ASSOCIATED MOLECULE / CRAM / COLLAPSIN RESPONSE MEDIATOR PROTEIN 5 / CRMP-5 / UNC33- ...DRP-5 / CRMP3-ASSOCIATED MOLECULE / CRAM / COLLAPSIN RESPONSE MEDIATOR PROTEIN 5 / CRMP-5 / UNC33-LIKE PHOSPHOPROTEIN 6 / ULIP-6


Mass: 52953.496 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9BPU6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.28 Å3/Da / Density % sol: 46.08 % / Description: NONE
Crystal growpH: 5 / Details: 23% (V/V) PEG 400 MMT PH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→51.1 Å / Num. obs: 110493 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 7 % / Biso Wilson estimate: 22.608 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / % possible all: 87.1

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GSE

2gse


Resolution: 1.7→39.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.121 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20181 5532 5 %RANDOM
Rwork0.17008 ---
obs0.17168 104852 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.592 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20 Å2
2---0.92 Å20 Å2
3---1.85 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7286 0 0 582 7868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197646
X-RAY DIFFRACTIONr_bond_other_d0.0070.027367
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.95110427
X-RAY DIFFRACTIONr_angle_other_deg1.3316987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27951012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55223.963323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.143151312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8531545
X-RAY DIFFRACTIONr_chiral_restr0.120.21204
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218717
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021710
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 30023 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 324 -
Rwork0.297 6462 -
obs--82.84 %

+
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