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- PDB-4cns: Crystal structure of truncated human CRMP-4 -

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Basic information

Entry
Database: PDB / ID: 4cns
TitleCrystal structure of truncated human CRMP-4
ComponentsDIHYDROPYRIMIDINASE-LIKE 3
KeywordsSIGNALING PROTEIN / NEUROGENESIS / AXONAL OUTGROWTH / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


filamin binding / chondroitin sulfate binding / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / actin crosslink formation / exocytic vesicle / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / CRMPs in Sema3A signaling / positive regulation of filopodium assembly / filamentous actin / cellular response to cytokine stimulus ...filamin binding / chondroitin sulfate binding / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / actin crosslink formation / exocytic vesicle / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / CRMPs in Sema3A signaling / positive regulation of filopodium assembly / filamentous actin / cellular response to cytokine stimulus / actin filament bundle assembly / neuron development / response to axon injury / negative regulation of cell migration / phosphoprotein binding / positive regulation of neuron projection development / SH3 domain binding / lamellipodium / negative regulation of neuron projection development / growth cone / cell body / synapse / extracellular space / identical protein binding / cytosol / cytoplasm
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 ...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
DI(HYDROXYETHYL)ETHER / Dihydropyrimidinase-related protein 3 / Dihydropyrimidinase-like 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPonnusamy, R. / 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 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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-LIKE 3
B: DIHYDROPYRIMIDINASE-LIKE 3
C: DIHYDROPYRIMIDINASE-LIKE 3
D: DIHYDROPYRIMIDINASE-LIKE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,08217
Polymers210,5264
Non-polymers55613
Water10,719595
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DIHYDROPYRIMIDINASE-LIKE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9027
Polymers52,6321
Non-polymers2706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: DIHYDROPYRIMIDINASE-LIKE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6913
Polymers52,6321
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: DIHYDROPYRIMIDINASE-LIKE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7974
Polymers52,6321
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: DIHYDROPYRIMIDINASE-LIKE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6913
Polymers52,6321
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.400, 89.620, 133.100
Angle α, β, γ (deg.)90.00, 101.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given)

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DIHYDROPYRIMIDINASE-LIKE 3


Mass: 52631.500 Da / Num. of mol.: 4 / Fragment: RESIDUES 13-490
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: Q8IXW6, UniProt: Q14195*PLUS

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Non-polymers , 5 types, 608 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 6.5
Details: 30% (W/V) PEG 3350, 100 MM NA TARTRATE, 100 MM BIS-TRIS PROPANE 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.04088
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: 1.04088 Å / Relative weight: 1
ReflectionResolution: 2.4→31.21 Å / Num. obs: 75030 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.8
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.4 / % possible all: 93.5

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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 4B91

4b91


Resolution: 2.4→30.99 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.89 / SU B: 15.526 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.593 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22581 3774 5 %RANDOM
Rwork0.18904 ---
obs0.19092 71230 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.372 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å21.15 Å2
2---1.08 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14706 0 28 595 15329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01915116
X-RAY DIFFRACTIONr_bond_other_d0.0070.0214359
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.95120503
X-RAY DIFFRACTIONr_angle_other_deg1.182333154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87751936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90925.023651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.517152593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0681562
X-RAY DIFFRACTIONr_chiral_restr0.080.22296
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117214
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023312
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_it0.9281.4467672
X-RAY DIFFRACTIONr_mcbond_other0.9291.4457671
X-RAY DIFFRACTIONr_mcangle_it1.5462.1649590
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1481.5587444
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
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 228 -
Rwork0.289 5062 -
obs--93.02 %
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)
10.3649-0.0165-0.11950.31250.01760.3162-0.003-0.01820.00490.04960.0113-0.0355-0.01050.0255-0.00820.0188-0.0001-0.01820.0027-0.00050.0202-3.3783-12.5415-64.1958
20.3374-0.0345-0.13040.4728-0.05710.50570.0260.0902-0.0339-0.0698-0.0164-0.01540.0417-0.0162-0.00960.01630.00730.00160.0314-0.02070.02394.6216-31.4711-109.5376
30.5309-0.0175-0.20110.46820.01620.27270.00310.05510.0686-0.035-0.0038-0.0483-0.0269-0.00020.00070.03380.00030.00660.03390.020.02193.63027.5825-112.6507
40.45290.0488-0.06070.22590.06150.43790.0040.03740.0003-0.02870.00390.01850.0108-0.0214-0.00790.00520.0003-0.00450.005500.0282-35.6455-6.9303-85.4996
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 489
2X-RAY DIFFRACTION2B12 - 488
3X-RAY DIFFRACTION3C11 - 488
4X-RAY DIFFRACTION4D11 - 489

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