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- PDB-4b3z: Structure of the human collapsin response mediator protein-1, a l... -

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Basic information

Entry
Database: PDB / ID: 4b3z
TitleStructure of the human collapsin response mediator protein-1, a lung cancer suppressor
ComponentsDIHYDROPYRIMIDINASE-RELATED PROTEIN 1
KeywordsHYDROLASE / SEMAPHORIN 3A / TIM BARREL / NON-SMALL-CELL LUNG CANCER / LUNG CANCER SUPPRESSOR
Function / homology
Function and homology information


filamin binding / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / CRMPs in Sema3A signaling / nucleobase-containing compound metabolic process / semaphorin-plexin signaling pathway / regulation of postsynapse assembly / phosphoprotein binding / spindle / nervous system development / presynapse ...filamin binding / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / CRMPs in Sema3A signaling / nucleobase-containing compound metabolic process / semaphorin-plexin signaling pathway / regulation of postsynapse assembly / phosphoprotein binding / spindle / nervous system development / presynapse / actin cytoskeleton / negative regulation of neuron projection development / growth cone / midbody / perikaryon / postsynapse / dendrite / centrosome / 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 ...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 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsLiu, S.H. / Lin, Y.H. / Huang, S.F. / Niou, Y.K. / Huang, L.L. / Chen, Y.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of Human Collapsin Response Mediator Protein 1: A Possible Role of its C-Terminal Tail.
Authors: Liu, S.H. / Huang, S.F. / Hsu, Y.L. / Pan, S.H. / Chen, Y.J. / Lin, Y.H.
History
DepositionJul 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Aug 19, 2015Group: Database references
Revision 1.4Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROPYRIMIDINASE-RELATED PROTEIN 1
B: DIHYDROPYRIMIDINASE-RELATED PROTEIN 1
C: DIHYDROPYRIMIDINASE-RELATED PROTEIN 1
D: DIHYDROPYRIMIDINASE-RELATED PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)249,0264
Polymers249,0264
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10220 Å2
ΔGint-33.2 kcal/mol
Surface area60090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.815, 147.846, 86.023
Angle α, β, γ (deg.)90.00, 94.61, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.8974, -0.3666, 0.2454), (-0.3524, 0.2611, -0.8987), (0.2654, -0.893, -0.3635)275.2505, 66.2227, -16.8576
2given(0.2737, -0.2879, -0.9177), (-0.2771, -0.9373, 0.2114), (-0.9211, 0.1964, -0.3363)126.28, 21.6912, 168.5239
3given(-0.3601, 0.6453, 0.6737), (0.6379, -0.3566, 0.6825), (0.6807, 0.6756, -0.2833)193.5232, -120.6642, -68.1703

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Components

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


Mass: 62256.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14194

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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: 2.15 Å3/Da / Density % sol: 42.9 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN SOLUTION AT 10 MG/ML IN 20 MM TRIS-HCL WITH 150 MM NACL, PH 7.5 AND THE WELL SOLUTION (50 MM AMMONIUM SULFATE, 50 MM SODIUM CITRATE, 12-15% PEG 8000) IN A 1:1 RATIO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.549
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.549 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 42140 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 58.03 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.38
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.3 / % possible all: 91.1

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Processing

Software
NameClassification
HKL-2000data reduction
CCP4phasing
PHENIXphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1KCX AND 2VM8

1kcx

2vm8


Resolution: 3.05→39.184 Å / SU ML: 0.69 / σ(F): 1.39 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 1176 2.8 %
Rwork0.1739 --
obs0.1754 42140 99.6 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 9.595 Å2 / ksol: 0.283 e/Å3
Displacement parametersBiso mean: 60.69 Å2
Baniso -1Baniso -2Baniso -3
1-4.9182 Å20 Å22.2684 Å2
2--1.7546 Å20 Å2
3----6.6729 Å2
Refinement stepCycle: LAST / Resolution: 3.05→39.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14530 0 0 0 14530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914828
X-RAY DIFFRACTIONf_angle_d1.13220105
X-RAY DIFFRACTIONf_dihedral_angle_d13.0435419
X-RAY DIFFRACTIONf_chiral_restr0.0732268
X-RAY DIFFRACTIONf_plane_restr0.0052599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.18880.33491330.24554651X-RAY DIFFRACTION96
3.1888-3.35680.28551410.22354809X-RAY DIFFRACTION99
3.3568-3.5670.30061320.20194828X-RAY DIFFRACTION99
3.567-3.84220.22631480.17434790X-RAY DIFFRACTION99
3.8422-4.22840.20151270.15234808X-RAY DIFFRACTION98
4.2284-4.83930.17951340.13284860X-RAY DIFFRACTION99
4.8393-6.09330.19571390.17324902X-RAY DIFFRACTION100
6.0933-39.18680.21811540.16864936X-RAY DIFFRACTION100

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