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- PDB-4h87: Crystal structure of a FHA domain of kanadaptin (SLC4A1AP) from H... -

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Basic information

Entry
Database: PDB / ID: 4h87
TitleCrystal structure of a FHA domain of kanadaptin (SLC4A1AP) from Homo sapiens at 1.55 A resolution
ComponentsKanadaptin
KeywordsPEPTIDE BINDING PROTEIN / FHA domain of PF00498 / mRNA processing / nucleus / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


intracellular membrane-bounded organelle / mRNA binding / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a FHA domain of kanadaptin (SLC4A1AP) from Homo sapiens at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Refinement description
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kanadaptin
B: Kanadaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,24113
Polymers28,2042
Non-polymers1,03711
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-94 kcal/mol
Surface area12550 Å2
MethodPISA
2
A: Kanadaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8559
Polymers14,1021
Non-polymers7538
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Kanadaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3864
Polymers14,1021
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.768, 82.141, 82.467
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kanadaptin / Human lung cancer oncogene 3 protein / HLC-3 / Kidney anion exchanger adapter protein / Solute ...Human lung cancer oncogene 3 protein / HLC-3 / Kidney anion exchanger adapter protein / Solute carrier family 4 anion exchanger member 1 adapter protein


Mass: 14101.977 Da / Num. of mol.: 2 / Fragment: FHA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLC3, NM_018158, SLC4A1AP / Plasmid: SGC_M / Production host: Escherichia Coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9BWU0
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG CONTAINING 6HIS-HA-FLAG-TEV SITES - ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG CONTAINING 6HIS-HA-FLAG-TEV SITES - MHHHHHHYPYDVPDYADYKDDDDKENLYFQSM. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY (-1) SER-MET (0) FOLLOWED BY RESIDUES 149-276 OF THE TARGET SEQUENCE.

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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: 2.09 Å3/Da / Density % sol: 41.08 %
Description: THE INPUT MODEL WAS PREPARED USING PHENIX.ROSETTA FOLLOWING THE PROCEDURE USED IN THE JCSG MR-PIPELINE (PMID: 18094477)
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.60M ammonium sulfate, 0.1M citric acid pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97932
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.55→36.764 Å / Num. obs: 35157 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.678 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 27.74
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.55-1.610.8852.9359513706199.8
1.61-1.670.5934.43365432171100
1.67-1.750.4096.2375503641199.9
1.75-1.840.2599.6335633370199.9
1.84-1.950.16414.2326763310199.8
1.95-2.10.10422363833473199.9
2.1-2.310.07130.9359513519199.9
2.31-2.650.05240.8363283610199.9
2.65-3.330.03359.8355843530199.9
3.33-36.7640.02180.6357853781199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
MOLREP11.0.02phasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
PHENIXphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ELS

3els


Resolution: 1.55→36.764 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.9492 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. SO4 AND GOL MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 3. ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. SO4 AND GOL MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 3. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS)
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 1759 5.01 %RANDOM
Rwork0.1755 ---
obs0.1767 35081 99.88 %-
Displacement parametersBiso max: 104.2 Å2 / Biso mean: 26.6599 Å2 / Biso min: 11.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.0815 Å20 Å20 Å2
2---1.2695 Å20 Å2
3---2.3509 Å2
Refine analyzeLuzzati coordinate error obs: 0.183 Å
Refinement stepCycle: LAST / Resolution: 1.55→36.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 60 207 2156
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d911SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes21HARMONIC2
X-RAY DIFFRACTIONt_gen_planes333HARMONIC5
X-RAY DIFFRACTIONt_it2086HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion256SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2496SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2086HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2856HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion4.2
X-RAY DIFFRACTIONt_other_torsion2.44
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2162 120 4.22 %
Rwork0.2029 2721 -
all0.2035 2841 -
obs--99.88 %
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)
11.7414-0.26090.0211.76520.41152.0683-0.0922-0.01690.0671-0.01730.09570.01540.03870.0225-0.0034-0.0423-0.00730.0041-0.0586-0.0148-0.046921.66239.3101-1.2001
21.5851-0.17050.92511.30950.09861.44330.0494-0.09280.0677-0.0339-0.0093-0.0301-0.03590.0203-0.0401-0.0188-0.00950.0026-0.0301-0.0189-0.0569.355754.3154-21.7192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|-1 - 276}A-1 - 276
2X-RAY DIFFRACTION2{B|-1 - 276}B-1 - 276

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