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- PDB-4cnt: CRYSTAL STRUCTURE OF WT HUMAN CRMP-4 -

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Basic information

Entry
Database: PDB / ID: 4cnt
TitleCRYSTAL STRUCTURE OF WT HUMAN CRMP-4
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 / filamin binding / chondroitin sulfate binding / actin crosslink formation / exocytic vesicle / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / CRMPs in Sema3A signaling / positive regulation of filopodium assembly / cellular response to cytokine stimulus / filamentous actin ...hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / filamin binding / chondroitin sulfate binding / actin crosslink formation / exocytic vesicle / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / CRMPs in Sema3A signaling / positive regulation of filopodium assembly / cellular response to cytokine stimulus / filamentous actin / actin filament bundle assembly / response to axon injury / neuron development / negative regulation of cell migration / positive regulation of neuron projection development / SH3 domain binding / lamellipodium / negative regulation of neuron projection development / cell body / growth cone / synapse / extracellular space / identical protein binding / cytoplasm / 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 / Dihydropyrimidinase-like 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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_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_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_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-LIKE 3
B: DIHYDROPYRIMIDINASE-LIKE 3
C: DIHYDROPYRIMIDINASE-LIKE 3
D: DIHYDROPYRIMIDINASE-LIKE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,2826
Polymers248,1974
Non-polymers852
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-44.5 kcal/mol
Surface area62830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.370, 157.650, 86.380
Angle α, β, γ (deg.)90.00, 113.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA12 - 49512 - 495
21PROPROBB12 - 49512 - 495
12ARGARGAA12 - 49612 - 496
22ARGARGCC12 - 49612 - 496
13ARGARGAA12 - 49612 - 496
23ARGARGDD12 - 49612 - 496
14PROPROBB12 - 49512 - 495
24PROPROCC12 - 49512 - 495
15PROPROBB12 - 49512 - 495
25PROPRODD12 - 49512 - 495
16ARGARGCC12 - 49612 - 496
26ARGARGDD12 - 49612 - 496

NCS ensembles :
ID
1
2
3
4
5
6
/ NCS oper: (Code: given)

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Components

#1: Protein
DIHYDROPYRIMIDINASE-LIKE 3 / DIHYDROPYRIMIDINASE-RELATED PROTEIN 3


Mass: 62049.148 Da / Num. of mol.: 4
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
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.13 Å3/Da / Density % sol: 42.4 % / Description: NONE
Crystal growpH: 7.5
Details: 15% (W/V) PEG 6000, 100 MM NAHEPES PH 7.5, 100 MM KCL

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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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.685
11L, -K, H20.315
ReflectionResolution: 2.66→43.79 Å / Num. obs: 61101 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 5.5
Reflection shellResolution: 2.66→2.72 Å / Redundancy: 3 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1 / % possible all: 99.5

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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 4CNS

4cns


Resolution: 2.65→55.97 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.886 / SU B: 16.487 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23563 3047 5 %RANDOM
Rwork0.18675 ---
obs0.18913 58196 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.723 Å2
Baniso -1Baniso -2Baniso -3
1--36.21 Å20 Å217.73 Å2
2--39.81 Å20 Å2
3----3.61 Å2
Refinement stepCycle: LAST / Resolution: 2.65→55.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14932 0 5 11 14948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01915247
X-RAY DIFFRACTIONr_bond_other_d0.0090.0214444
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.9520679
X-RAY DIFFRACTIONr_angle_other_deg1.328333326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01851937
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62424.97660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59152584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8641564
X-RAY DIFFRACTIONr_chiral_restr0.0810.22316
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02117367
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023345
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_it3.573.9487760
X-RAY DIFFRACTIONr_mcbond_other3.573.9487759
X-RAY DIFFRACTIONr_mcangle_it5.4095.9189693
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3684.1137487
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

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A305770.08
12B305770.08
21A304700.09
22C304700.09
31A305690.09
32D305690.09
41B303690.08
42C303690.08
51B306060.08
52D306060.08
61C305330.08
62D305330.08
LS refinement shellResolution: 2.655→2.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 205 -
Rwork0.329 4236 -
obs--98.23 %
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)
10.42280.0232-0.07340.3352-0.05490.1415-0.0341-0.0192-0.05660.00390.0220.00060.047-0.00840.01210.1378-0.0107-0.02270.00380.00630.095-16.4719-15.2703-29.02
20.35760.1049-0.04450.26980.05390.11540.0040.0220.1576-0.02140.02460.03070.0153-0.0091-0.02850.0482-0.0015-0.00520.00560.02070.1885-7.849132.4407-34.6215
30.43960.1576-0.27970.19-0.14180.28930.0277-0.14540.0185-0.0284-0.04-0.0334-0.01330.08070.01230.0562-0.0116-0.05220.0532-0.01810.122723.799616.9563-19.0218
40.35280.1885-0.17410.32-0.03850.1794-0.0011-0.1093-0.00210.0313-0.01250.02770.00260.05810.01360.0981-0.0024-0.01270.1076-0.0070.0113-14.56470.04816.3749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 496
2X-RAY DIFFRACTION2B12 - 497
3X-RAY DIFFRACTION3C12 - 496
4X-RAY DIFFRACTION4D12 - 496

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