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- PDB-4l0r: Crystal structure of FGF2-interacting protein from Homo sapiens. ... -

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Basic information

Entry
Database: PDB / ID: 4l0r
TitleCrystal structure of FGF2-interacting protein from Homo sapiens. Northeast Structural Genomics Consortium Target HR9027A.
ComponentsCentrosomal protein of 57 kDa
KeywordsCELL CYCLE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / Cep57 / Centrosomal protein
Function / homology
Function and homology information


ciliary basal body-plasma membrane docking / microtubule anchoring / gamma-tubulin binding / fibroblast growth factor binding / spermatid development / fibroblast growth factor receptor signaling pathway / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes ...ciliary basal body-plasma membrane docking / microtubule anchoring / gamma-tubulin binding / fibroblast growth factor binding / spermatid development / fibroblast growth factor receptor signaling pathway / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of G2/M transition of mitotic cell cycle / AURKA Activation by TPX2 / protein homooligomerization / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / microtubule binding / microtubule / centrosome / Golgi apparatus / protein homodimerization activity / nucleus / cytosol
Similarity search - Function
Centrosomal protein 57kDa / Cep57 centrosome microtubule-binding domain / Cep57 centrosome localisation domain / Centrosome microtubule-binding domain of Cep57 / Centrosome localisation domain of Cep57 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Centrosomal protein of 57 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å
AuthorsSeetharaman, J. / Lew, S. / Su, M. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. ...Seetharaman, J. / Lew, S. / Su, M. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of FGF2-interacting protein from Homo sapiens. Northeast Structural Genomics consortium id HR9027A
Authors: Seetharaman, J. / Lew, S. / Su, M. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionMay 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centrosomal protein of 57 kDa
B: Centrosomal protein of 57 kDa


Theoretical massNumber of molelcules
Total (without water)25,3812
Polymers25,3812
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.121, 70.097, 31.331
Angle α, β, γ (deg.)90.00, 94.81, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 33 - 104 / Label seq-ID: 33 - 104

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

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Components

#1: Protein Centrosomal protein of 57 kDa / Cep57 / FGF2-interacting protein / Testis-specific protein 57 / Translokin


Mass: 12690.426 Da / Num. of mol.: 2 / Fragment: UNP residues 334-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP57, KIAA0092, TSP57 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86XR8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 6
Details: 0.1 M KAcetate, 0.1 M MES, PEG 1000 40% (w/v), pH 6, Microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 8715 / Num. obs: 8351 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.095 / Rsym value: 0.079 / Net I/σ(I): 11.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.29 / % possible all: 79.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.49→34.04 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.841 / SU B: 8.508 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.451 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 346 4.6 %RANDOM
Rwork0.22224 ---
obs0.22441 7133 83.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.411 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å2-0 Å2-0.28 Å2
2---0.71 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.49→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 0 59 1240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191189
X-RAY DIFFRACTIONr_bond_other_d0.0040.021182
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9871590
X-RAY DIFFRACTIONr_angle_other_deg1.10832736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7665145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22527.4663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.5215254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.941154
X-RAY DIFFRACTIONr_chiral_restr0.0650.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021343
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02241
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: 3787 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.486→2.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 9 -
Rwork0.202 214 -
obs--33.09 %

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