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- PDB-3qij: Primitive-monoclinic crystal structure of the FERM domain of prot... -

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Basic information

Entry
Database: PDB / ID: 3qij
TitlePrimitive-monoclinic crystal structure of the FERM domain of protein 4.1R
ComponentsProtein 4.1
KeywordsSTRUCTURAL PROTEIN / cytoskeleton / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


1-phosphatidylinositol binding / regulation of intestinal absorption / spectrin-associated cytoskeleton / actomyosin structure organization / Neurexins and neuroligins / cortical actin cytoskeleton organization / spectrin binding / intercellular bridge / cortical cytoskeleton / regulation of calcium ion transport ...1-phosphatidylinositol binding / regulation of intestinal absorption / spectrin-associated cytoskeleton / actomyosin structure organization / Neurexins and neuroligins / cortical actin cytoskeleton organization / spectrin binding / intercellular bridge / cortical cytoskeleton / regulation of calcium ion transport / positive regulation of protein localization to cell cortex / phosphoprotein binding / structural constituent of cytoskeleton / cytoplasmic side of plasma membrane / mitotic spindle / positive regulation of protein binding / cell junction / actin binding / cell cortex / actin cytoskeleton organization / basolateral plasma membrane / protein-containing complex assembly / cytoskeleton / nuclear body / calmodulin binding / cell cycle / cell division / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
Band 4.1 protein, chordates / SAB domain / Band 4.1, C-terminal / SAB domain / 4.1 protein C-terminal domain (CTD) / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like ...Band 4.1 protein, chordates / SAB domain / Band 4.1, C-terminal / SAB domain / 4.1 protein C-terminal domain (CTD) / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsNedyalkova, L. / Zhong, N. / Tong, Y. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Primitive-monoclinic crystal structure of the FERM domain of protein 4.1R
Authors: Nedyalkova, L. / Zhong, N. / Tong, Y. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionJan 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein 4.1
B: Protein 4.1


Theoretical massNumber of molelcules
Total (without water)68,86321
Polymers68,8632
Non-polymers019
Water3,963220
1
A: Protein 4.1


Theoretical massNumber of molelcules
Total (without water)34,43211
Polymers34,4321
Non-polymers010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein 4.1


Theoretical massNumber of molelcules
Total (without water)34,43210
Polymers34,4321
Non-polymers09
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.001, 53.469, 88.766
Angle α, β, γ (deg.)90.000, 106.960, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL MOLECULE IS UNKNOWN.

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Components

#1: Protein Protein 4.1 / P4.1 / 4.1R / Band 4.1 / EPB4.1


Mass: 34431.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPB41, E41P / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: P11171
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 19 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.2M magnesium chloride, 1% w/w dispase-I, pH 7.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98322 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98322 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 51901 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.055 / Χ2: 1.043 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.833.50.98925090.79197.1
1.83-1.863.70.83525660.799100
1.86-1.93.70.65225980.839100
1.9-1.943.70.52526070.886100
1.94-1.983.70.41825700.911100
1.98-2.033.70.33125730.912100
2.03-2.083.70.26425790.93100
2.08-2.133.70.22126130.997100
2.13-2.23.70.17625520.98100
2.2-2.273.70.14826201.104100
2.27-2.353.70.12325761.009100
2.35-2.443.70.11425911.11699.9
2.44-2.553.70.08525961.034100
2.55-2.693.70.07526121.11100
2.69-2.863.70.06625791.24399.7
2.86-3.083.60.04826121.336100
3.08-3.393.60.03626141.303100
3.39-3.883.50.02626301.228100
3.88-4.883.60.02326331.18299.9
4.88-503.60.02426711.13498.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1gg3

1gg3


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.202 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.195 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. The programs coot, buccaneer, arp/warp were used during refinement as well as the molprobity server.
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 2029 3.927 %thin shells (SFTOOLS)
Rwork0.2067 ---
obs0.209 51670 99.747 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 80.04 Å2 / Biso mean: 25.977 Å2 / Biso min: 13.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.086 Å20 Å20.056 Å2
2--1.283 Å20 Å2
3----1.164 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4277 0 19 220 4516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224400
X-RAY DIFFRACTIONr_bond_other_d0.0010.022938
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9625976
X-RAY DIFFRACTIONr_angle_other_deg0.88137186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41424.225187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96515733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0371515
X-RAY DIFFRACTIONr_chiral_restr0.0910.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02899
X-RAY DIFFRACTIONr_mcbond_it0.8551.52716
X-RAY DIFFRACTIONr_mcbond_other0.2221.51089
X-RAY DIFFRACTIONr_mcangle_it1.53324365
X-RAY DIFFRACTIONr_scbond_it2.26231684
X-RAY DIFFRACTIONr_scangle_it3.4234.51608
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% reflection obs (%)
1.8-1.84700.3623794380499.737
1.847-1.8970.3222560.3023417368099.81
1.897-1.95200.2663597360199.889
1.952-2.0120.3042230.2393256348299.914
2.012-2.0770.2792300.2263160339899.765
2.077-2.1500.2143300330599.849
2.15-2.230.2891730.2052973315099.873
2.23-2.3210.2591760.2052885306999.739
2.321-2.4240.291450.2072779293199.761
2.424-2.54100.2022793279999.786
2.541-2.6770.2811370.2122518266099.812
2.677-2.8380.2561270.2322389252799.565
2.838-3.0320.2671110.2212274238699.958
3.032-3.2730.263970.2082126222799.82
3.273-3.5810.21740.1941976205499.805
3.581-3.9960.215720.1721781185599.892
3.996-4.6010.224910.1561562165799.759
4.601-5.6020.267360.1711385142599.719
5.602-7.7880.303660.2271050111999.732
7.788-300.249150.20162667295.387
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)
11.49760.79971.21451.53211.44313.19280.0529-0.0570.14970.0273-0.1010.0955-0.1087-0.18550.04810.0529-0.00860.04830.0896-0.01380.103714.70284.026179.0759
20.96650.09720.42811.23720.86452.7027-0.08470.1956-0.0214-0.09970.0783-0.03050.02970.17550.00630.0357-0.01220.02810.08190.01220.072434.6911-12.84850.7994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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