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Basic information

Entry
Database: PDB / ID: 1vka
TitleSoutheast Collaboratory for Structural Genomics: Hypothetical Human Protein Q15691 N-Terminal Fragment
ComponentsMicrotubule-associated protein RP/EB family member 1
KeywordsStructural Genomics / unknown function / Q15691 / Homo sapiens / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


protein localization to mitotic spindle / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / mitotic spindle microtubule / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding ...protein localization to mitotic spindle / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / mitotic spindle microtubule / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / protein localization to centrosome / microtubule organizing center / negative regulation of microtubule polymerization / mitotic spindle pole / cytoplasmic microtubule / establishment of mitotic spindle orientation / microtubule polymerization / spindle midzone / spindle assembly / regulation of microtubule polymerization or depolymerization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / EML4 and NUDC in mitotic spindle formation / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of microtubule polymerization / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / protein localization / cell migration / microtubule / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / RNA binding / identical protein binding / cytosol
Similarity search - Function
EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily ...EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / sulfur sas / SAD / Resolution: 1.6 Å
AuthorsLiu, Z.-J. / Tempel, W. / Schubot, F.D. / Shah, A. / Dailey, T.A. / Mayer, M.R. / Rose, J.P. / Dailey, H.A. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: TO BE PUBLISHED
Title: Southeast Collaboratory for Structural Genomics: Hypothetical Human Protein Q15691 N-Terminal Fragment
Authors: Liu, Z.-J. / Tempel, W. / SCHUBOT, F.D. / SHAH, A. / ROSE, J.P. / RICHARDSON, D.C. / RICHARDSON, J.S. / Wang, B.-C.
History
DepositionMay 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE THE STRUCTURE PRESENTED IN THIS ENTRY IS A PROTOLYTIC FRAGMENT (RESIDUES (2-140) OF THE ...SEQUENCE THE STRUCTURE PRESENTED IN THIS ENTRY IS A PROTOLYTIC FRAGMENT (RESIDUES (2-140) OF THE MATURE Q15691 PROTEIN.
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated protein RP/EB family member 1
B: Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)34,7922
Polymers34,7922
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.951, 47.582, 100.690
Angle α, β, γ (deg.)90.000, 91.741, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1


Mass: 17395.861 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: The protein was cloned, expressed and purified by the SECSG human protein production group (T.A. Dailey, M. Mayer) under the direction H.A. Dailey.
Gene: MAPRE1 / Cell line (production host): BL21(DE53) / Production host: Escherichia coli (E. coli) / Keywords: APC-binding protein, Q15691, sulfur SAS / References: UniProt: Q15691
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: clear colorless prism
Crystal growTemperature: 291 K / Method: micro-batch under oil / pH: 6.2 / Details: pH 6.2, Micro-batch under oil, temperature 291K

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Data collection

Diffraction
IDCrystal-ID
q156911
11
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2003
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 37287 / % possible obs: 98.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.2
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obs
1.6-1.6696.70.107
3.45-5093.70.033
2.74-3.4599.50.036
2.39-2.7499.60.039
2.17-2.3999.30.041
2.02-2.1799.10.045
1.9-2.0298.80.052
1.8-1.998.60.062
1.72-1.898.30.073
1.66-1.7298.20.087

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 3 Å / D res low: 20 Å / FOM : 0.38 / Reflection: 4962
Phasing MAD shell
Resolution (Å)FOM Reflection
9.91-200.34158
6.56-9.910.41446
5.22-6.560.39545
4.46-5.220.38631
3.96-4.460.38703
3.6-3.960.39777
3.32-3.60.36822
3.09-3.320.35880
Phasing dmFOM : 0.59 / FOM acentric: 0.63 / FOM centric: 0.4 / Reflection: 5492 / Reflection acentric: 4544 / Reflection centric: 948
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.3-9.9730.780.780.51147539
5.2-8.30.630.720.38780586194
4.1-5.20.690.750.46960772188
3.6-4.10.70.730.57946787159
3.1-3.60.580.620.3516741439235
2.9-3.10.350.360.221018885133

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefmac_5.1.24refinement
HKL-2000data reduction
ARP/wARPmodel building
RefinementMethod to determine structure: sulfur sas / Resolution: 1.6→100 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.367 / SU ML: 0.05 / SU R Cruickshank DPI: 0.093 / ESU R Free: 0.086
Details: THE Q15691 STRUCTURE WAS INITIALLY SOLVED TO 3 ANGSTROMS IN SPACE GROUP P 21 21 21 USING A SET OF SULFUR SAS DATA COLLECTED WITH FOCUSED CHROMIUM X-RAYS (LAMBDA = 2.29 ANGSTROMS). THE MODEL ...Details: THE Q15691 STRUCTURE WAS INITIALLY SOLVED TO 3 ANGSTROMS IN SPACE GROUP P 21 21 21 USING A SET OF SULFUR SAS DATA COLLECTED WITH FOCUSED CHROMIUM X-RAYS (LAMBDA = 2.29 ANGSTROMS). THE MODEL PRESENTED IN THIS ENTRY WAS REFINED AGAINST 1.6 ANGSTROM DATA COLLECTED AT SER-CAT (22ID) ON A BETTER DIFFRACTING MONOCLINIC CRYSTAL.
RfactorNum. reflection% reflection
Rfree0.2137 1964 5.004 %
Rwork0.1998 --
all0.201 --
obs-37287 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 15.686 Å2
Baniso -1Baniso -2Baniso -3
1--0.551 Å20 Å2-0.078 Å2
2--0.595 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 0 201 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222120
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9312866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8715262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.0860.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021615
X-RAY DIFFRACTIONr_nbd_refined0.1930.2953
X-RAY DIFFRACTIONr_nbtor_refined0.310.21535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2125
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.25
X-RAY DIFFRACTIONr_mcbond_it0.741.51303
X-RAY DIFFRACTIONr_mcangle_it1.3622086
X-RAY DIFFRACTIONr_scbond_it2.1353817
X-RAY DIFFRACTIONr_scangle_it3.3374.5780
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.599-1.64080.2391360.19525292927
1.641-1.68580.2221460.18627152926
1.686-1.73460.2021460.18625682754
1.735-1.7880.2311120.225562721
1.788-1.84660.2311440.19724482628
1.847-1.91140.2231300.19623932556
1.911-1.98350.2481200.19923422496
1.984-2.06450.231110.19921862316
2.064-2.15620.2151060.20221592287
2.156-2.26140.1981050.20320692192
2.261-2.38370.1761040.19619522068
2.384-2.52820.193890.19918581956
2.528-2.70260.2131020.20617441852
2.703-2.9190.215870.21216261720
2.919-3.19730.205960.20115101613
3.197-3.57420.24740.20413401436
3.574-4.12630.204600.18611701266
4.126-5.05150.186430.18310081089
5.052-7.13480.228390.217775852
7.135-1000.262140.266339486

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