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- PDB-4q04: Crystal structure of URE3-BP from Entomaeba histolytica without c... -

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Basic information

Entry
Database: PDB / ID: 4q04
TitleCrystal structure of URE3-BP from Entomaeba histolytica without calcium
ComponentsURE3-BP sequence specific DNA binding protein
KeywordsDNA BINDING PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / sequence specific / calcium dependent inhibition / transcription factor / TRANSCRIPTION
Function / homology
Function and homology information


calcium-dependent protein binding / calcium ion binding / cytoplasm
Similarity search - Function
: / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...: / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
URE3-BP sequence specific DNA binding protein
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of URE3-BP from Entomaeba histolytica
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: URE3-BP sequence specific DNA binding protein
B: URE3-BP sequence specific DNA binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7937
Polymers51,5342
Non-polymers2585
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-60 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.420, 69.420, 187.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-416-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein URE3-BP sequence specific DNA binding protein


Mass: 25767.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: URE3-BP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GSV7

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Non-polymers , 5 types, 290 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: EnhiA.01648.a.D11.PD00049 at 11.96 mg/mL against Precipitant Synergy block 2, 20.1% PEG 1500, 2.01% MPD, 0.2 M magnesium sulfate, 0.1 M sodium acetate pH 5.5, crystal tracking ID 248792c5, ...Details: EnhiA.01648.a.D11.PD00049 at 11.96 mg/mL against Precipitant Synergy block 2, 20.1% PEG 1500, 2.01% MPD, 0.2 M magnesium sulfate, 0.1 M sodium acetate pH 5.5, crystal tracking ID 248792c5, unique puck ID cjw8-9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 21, 2013 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 37199 / Num. obs: 33977 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 25.002 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1.014 / Net I/σ(I): 20.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.950.2393.184746239089.6
1.95-20.2084.286567247693.5
2-2.060.1786.118343241194.4
2.06-2.120.1618.4411119236295.1
2.12-2.190.14911.1214361226494.7
2.19-2.270.12314.2215198221294.4
2.27-2.360.11515.6114675212494
2.36-2.450.117.8314145203493.2
2.45-2.560.08920.0413606195292.9
2.56-2.690.07822.3212859185092.3
2.69-2.830.07324.5912210174091.3
2.83-30.06626.0311784166690.8
3-3.210.05729.9510858154090
3.21-3.470.0534.910168144889
3.47-3.80.04240.599061131188.3
3.8-4.250.03844.848154117886.7
4.25-4.910.03347.757418104585.7
4.91-6.010.0343.52644787783.8
6.01-8.50.02841.92520069481.9
8.50.02151.14276040375.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.88 Å
Translation3.5 Å19.88 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SJS

3sjs


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.2257 / WRfactor Rwork: 0.1688 / FOM work R set: 0.8674 / SU B: 7.247 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1702 / SU Rfree: 0.1633 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 1720 5.1 %RANDOM
Rwork0.182 ---
obs0.1849 33961 91.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.19 Å2 / Biso mean: 19.677 Å2 / Biso min: 8.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 14 285 3748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023603
X-RAY DIFFRACTIONr_bond_other_d0.0020.023327
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9494897
X-RAY DIFFRACTIONr_angle_other_deg0.86937623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.535436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02223.254169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89815584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2511521
X-RAY DIFFRACTIONr_chiral_restr0.0970.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
X-RAY DIFFRACTIONr_mcbond_it1.0751.3911714
X-RAY DIFFRACTIONr_mcbond_other1.0751.391713
X-RAY DIFFRACTIONr_mcangle_it1.682.082142
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 112 -
Rwork0.246 2275 -
all-2387 -
obs--89.6 %
Refinement TLS params.

S21: -0.0126 Å ° / 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 °)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)
10.3997-0.12680.0330.78780.16410.5334-0.05370.01740.01050.0844-0.05460.03190.0423-0.03070.0172-0.00410.01070.0169-0.00380.033717.14713.871165.5373
20.50260.0539-0.02850.5426-0.0760.1722-0.02920.06090.03390.01340.01370.0204-0.05690.01580.0058-0.00780.00420.0413-0.0050.0163-14.44611.423676.074
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 220
2X-RAY DIFFRACTION2B7 - 220

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