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- PDB-4cnu: CRYSTAL STRUCTURE OF WT HUMAN CRMP-4 from lattice translocation -

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Basic information

Entry
Database: PDB / ID: 4cnu
TitleCRYSTAL STRUCTURE OF WT HUMAN CRMP-4 from lattice translocation
ComponentsDIHYDROPYRIMIDINASE-LIKE 3
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 / chondroitin sulfate binding / filamin binding / actin crosslink formation / exocytic vesicle / CRMPs in Sema3A signaling / positive regulation of filopodium assembly / cellular response to cytokine stimulus / filamentous actin / actin filament bundle assembly ...hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / chondroitin sulfate binding / filamin binding / actin crosslink formation / exocytic vesicle / CRMPs in Sema3A signaling / positive regulation of filopodium assembly / cellular response to cytokine stimulus / filamentous actin / actin filament bundle assembly / neuron development / response to axon injury / negative regulation of cell migration / positive regulation of neuron projection development / SH3 domain binding / negative regulation of neuron projection development / lamellipodium / cell body / growth cone / synapse / extracellular space / identical protein binding / 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 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPonnusamy, R. / Lebedev, A. / Lohkamp, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystal Structure of Human Crmp-4: Correction of Intensities for Lattice-Translocation Disorder
Authors: Ponnusamy, R. / Lebedev, A. / Pahlow, S. / Lohkamp, B.
History
DepositionJan 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROPYRIMIDINASE-LIKE 3
B: DIHYDROPYRIMIDINASE-LIKE 3


Theoretical massNumber of molelcules
Total (without water)124,0982
Polymers124,0982
Non-polymers00
Water0
1
A: DIHYDROPYRIMIDINASE-LIKE 3

A: DIHYDROPYRIMIDINASE-LIKE 3

B: DIHYDROPYRIMIDINASE-LIKE 3

B: DIHYDROPYRIMIDINASE-LIKE 3


Theoretical massNumber of molelcules
Total (without water)248,1974
Polymers248,1974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_546-x+1/2,y-1/2,-z+11
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area12900 Å2
ΔGint-52.3 kcal/mol
Surface area62230 Å2
MethodPISA
2
B: DIHYDROPYRIMIDINASE-LIKE 3

B: DIHYDROPYRIMIDINASE-LIKE 3

A: DIHYDROPYRIMIDINASE-LIKE 3

A: DIHYDROPYRIMIDINASE-LIKE 3


Theoretical massNumber of molelcules
Total (without water)248,1974
Polymers248,1974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
crystal symmetry operation3_556-x+1/2,y+1/2,-z+11
Buried area12900 Å2
ΔGint-52.3 kcal/mol
Surface area62230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.240, 108.220, 118.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 0 / Auth seq-ID: 12 - 499 / Label seq-ID: 12 - 499

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

NCS oper: (Code: given)

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Components

#1: Protein DIHYDROPYRIMIDINASE-LIKE 3 / DRP-3 / COLLAPSIN RESPONSE MEDIATOR PROTEIN 4 / CRMP-4 / UNC-33-LIKE PHOSPHOPROTEIN 1 / ULIP-1 / ...DRP-3 / COLLAPSIN RESPONSE MEDIATOR PROTEIN 4 / CRMP-4 / UNC-33-LIKE PHOSPHOPROTEIN 1 / ULIP-1 / DIHYDROPYRIMIDINASE-RELATED PROTEIN 3 / DIHYDROPYRIMIDINASE-LIKE 3


Mass: 62049.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q14195
Sequence detailsISOFORM 2 GENBANK REF NP_001378.1

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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: 2.43 Å3/Da / Density % sol: 49.3 % / Description: NONE
Crystal growpH: 7
Details: 23% (W/V) PEG 3350, 200 MM NA TARTRATE, 100 MM BIS-TRIS PROPANE PH 7.0, 50 MM NA FLUORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.07068
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 25, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07068 Å / Relative weight: 1
ReflectionResolution: 2.8→39.4 Å / Num. obs: 28951 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 4.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.2 / % possible all: 84.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CNS

4cns


Resolution: 2.8→39.43 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.898 / SU B: 17.095 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. DATA WERE CORRECTED FOR LATTICE TRANSLOCATION DISORDER ITERATIVELY BEFORE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.29484 1465 5.1 %RANDOM
Rwork0.25523 ---
obs0.25725 27454 93.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.273 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å20 Å2
2---1.53 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7512 0 0 0 7512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197670
X-RAY DIFFRACTIONr_bond_other_d0.0020.027258
X-RAY DIFFRACTIONr_angle_refined_deg0.9811.9510402
X-RAY DIFFRACTIONr_angle_other_deg0.698316746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6035974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62724.94332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.973151300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6571532
X-RAY DIFFRACTIONr_chiral_restr0.0550.21162
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021686
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_it1.4244.5933902
X-RAY DIFFRACTIONr_mcbond_other1.4214.5923901
X-RAY DIFFRACTIONr_mcangle_it2.4296.8834874
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1844.7243768
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: 31445 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.02 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 103 -
Rwork0.369 1785 -
obs--83.43 %

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