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- PDB-4b92: Crystal structure of truncated human CRMP-5 soaked with Zn -

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Basic information

Entry
Database: PDB / ID: 4b92
TitleCrystal structure of truncated human CRMP-5 soaked with Zn
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 / 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: 2.9 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 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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)106,1696
Polymers105,9072
Non-polymers2624
Water543
1
A: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
hetero molecules

A: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
hetero molecules

B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
hetero molecules

B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,33712
Polymers211,8144
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
crystal symmetry operation5_545-x+1/2,y-1/2,-z+1/41
crystal symmetry operation3_545-y+1/2,x-1/2,z+1/41
Buried area9500 Å2
ΔGint-274.8 kcal/mol
Surface area61200 Å2
MethodPISA
2
B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
hetero molecules

B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
hetero molecules

A: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
hetero molecules

A: DIHYDROPYRIMIDINASE-RELATED PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,33712
Polymers211,8144
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation4_554y+1/2,-x+1/2,z-1/41
crystal symmetry operation5_555-x+1/2,y+1/2,-z+1/41
Buried area9500 Å2
ΔGint-274.8 kcal/mol
Surface area61200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.500, 89.500, 246.460
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: _ / 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 - 481 / Label seq-ID: 9 - 482

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

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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: 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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.28 Å3/Da / Density % sol: 46.08 % / Description: NONE
Crystal growpH: 5 / Details: 23% (V/V) PEG 400 MMT PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.03873
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03873 Å / Relative weight: 1
ReflectionResolution: 2.9→39.3 Å / Num. obs: 23108 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7 % / Biso Wilson estimate: 70.549 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.6 / % 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: 2.9→38.92 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.594 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25009 1180 5.1 %RANDOM
Rwork0.19077 ---
obs0.19377 21826 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.298 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å20 Å2
2---2.19 Å20 Å2
3---4.37 Å2
Refinement stepCycle: LAST / Resolution: 2.9→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7300 0 4 3 7307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197452
X-RAY DIFFRACTIONr_bond_other_d0.0050.027166
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.95210102
X-RAY DIFFRACTIONr_angle_other_deg1.014316490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4145949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01124.065310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.949151267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.571542
X-RAY DIFFRACTIONr_chiral_restr0.0720.21167
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218401
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021637
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: 29976 / 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: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 98 -
Rwork0.277 1547 -
obs--99.88 %

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