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- PDB-4b90: Crystal structure of WT human CRMP-5 -

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Basic information

Entry
Database: PDB / ID: 4b90
TitleCrystal structure of WT human CRMP-5
ComponentsDIHYDROPYRIMIDINASE-RELATED PROTEIN 5
KeywordsSIGNALING PROTEIN / NEUROGENESIS / 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 / neuronal cell body / dendrite / glutamatergic synapse / 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: 2.2 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 / Derived calculations / 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 5
B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2484
Polymers128,1242
Non-polymers1242
Water3,225179
1
A: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)256,4968
Polymers256,2484
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12670 Å2
ΔGint-31.8 kcal/mol
Surface area63670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.150, 90.150, 247.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2072-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 8 - 490 / Label seq-ID: 30 - 512

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

NCS oper: (Code: given)

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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: 64062.008 Da / Num. of mol.: 2
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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1.97 Å3/Da / Density % sol: 37.45 % / Description: NONE
Crystal growpH: 6 / Details: 25% (W/V) PEG 1500 SPG PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→56.6 Å / Num. obs: 69984 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7 % / Biso Wilson estimate: 24.798 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 10.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B91

4b91


Resolution: 2.2→44.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 10.928 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22082 2686 5.1 %RANDOM
Rwork0.18023 ---
obs0.1823 49886 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.246 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å20 Å2
2---2.11 Å20 Å2
3---4.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7454 0 8 179 7641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197694
X-RAY DIFFRACTIONr_bond_other_d0.0060.027427
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.95310449
X-RAY DIFFRACTIONr_angle_other_deg1.129317097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6923.827324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.514151320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4271549
X-RAY DIFFRACTIONr_chiral_restr0.0950.21201
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218707
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021708
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: 30310 / 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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 199 -
Rwork0.263 3609 -
obs--99.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.31380.0447-0.04150.2202-0.04060.2320.0123-0.0577-0.03490.0298-0.0045-0.0193-0.01850.0062-0.00780.0820.0040.00850.1343-0.01080.009943.913142.865818.5746
20.54730.0990.03730.42380.09890.11740.00290.02150.0426-0.0166-0.00080.08130.0168-0.0065-0.00210.0769-0.00330.00570.1114-0.00580.02430.414325.15936.1336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 564
2X-RAY DIFFRACTION2B1 - 564

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