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- PDB-3sia: Crystal structure of URE3-binding protein, (D127A,N129A) mutant, ... -

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Basic information

Entry
Database: PDB / ID: 3sia
TitleCrystal structure of URE3-binding protein, (D127A,N129A) mutant, iodide phased
ComponentsURE3-BP sequence specific DNA binding protein
KeywordsDNA BINDING PROTEIN / EF-hand / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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
IODIDE ION / URE3-BP sequence specific DNA binding protein
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Skubak, P.
CitationJournal: To be Published
Title: Crystal structure of URE3-binding protein
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Gardberg, A. / Edwards, T. / Staker, B. / Skubak, P. / Stewart, L. / Gilchrist, C.
History
DepositionJun 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,09530
Polymers25,6801
Non-polymers3,41529
Water1,11762
1
A: URE3-BP sequence specific DNA binding protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)58,19060
Polymers51,3602
Non-polymers6,83058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9240 Å2
ΔGint-72 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.880, 68.250, 130.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-247-

IOD

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Components

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


Mass: 25679.996 Da / Num. of mol.: 1 / Mutation: D127A, N129A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: URE3-BP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9GSV7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Internal tracking number 218398G5. Focus screen based on CryoFull G6. 1.5 uL 40% PEG600, 0.1 M citrate pH 4.6 + 2 uL EnhiA.01648.a.D18 PD00157 (VCID3088) at 5.6 mg/ml, VAPOR DIFFUSION, ...Details: Internal tracking number 218398G5. Focus screen based on CryoFull G6. 1.5 uL 40% PEG600, 0.1 M citrate pH 4.6 + 2 uL EnhiA.01648.a.D18 PD00157 (VCID3088) at 5.6 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.05→26.86 Å / Num. obs: 13084 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 13.48 % / Biso Wilson estimate: 28.721 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 25.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.1100.3696.5824281886.4
2.1-2.160.3228.31125193997.8
2.16-2.220.26311.31242187598.6
2.22-2.290.22912.71299692099
2.29-2.370.188151169582499.4
2.37-2.450.19314.61198384699.4
2.45-2.540.16216.71148780699.4
2.54-2.650.13220.61079476199.5
2.65-2.760.11422.71091676599.7
2.76-2.90.09825.6996670899.7
2.9-3.060.08527.5969368099.9
3.06-3.240.07331.99151651100
3.24-3.470.05640.1872162399.8
3.47-3.740.04747.58126579100
3.74-4.10.04251.67334534100
4.1-4.580.04454.86546489100
4.58-5.290.04453.55408416100
5.29-6.480.04847.14498372100
6.48-9.170.04849.73372301100
9.170.03754.6182017794.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→26.86 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.081 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 637 4.9 %RANDOM
Rwork0.176 ---
obs0.179 13006 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.657 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.05→26.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 29 62 1792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221761
X-RAY DIFFRACTIONr_bond_other_d0.0010.021177
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9432397
X-RAY DIFFRACTIONr_angle_other_deg0.95632843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2235212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.07323.29382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47515269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.132159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02400
X-RAY DIFFRACTIONr_mcbond_it0.8961.51063
X-RAY DIFFRACTIONr_mcbond_other0.2551.5423
X-RAY DIFFRACTIONr_mcangle_it1.60821704
X-RAY DIFFRACTIONr_scbond_it2.8093698
X-RAY DIFFRACTIONr_scangle_it4.2424.5692
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 38 -
Rwork0.187 777 -
all-815 -
obs--86.43 %
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)
13.97913.6894-7.43733.2062-6.75712.9667-0.1494-0.2698-0.3275-0.1534-0.1171-0.07710.26650.47980.26650.26480.060.01950.11710.00290.109314.7537.3290.248
22.27690.4843-0.12422.6171-0.56262.4352-0.07060.2174-0.1044-0.07490.03060.046-0.0484-0.14640.040.01960.006-0.01120.05390.00730.04969.99718.1029.486
34.4838-1.08230.81692.08970.15912.6072-0.1071-0.151-0.1530.20060.04130.2518-0.1303-0.08380.06580.0792-0.020.00490.04690.00620.046811.69317.2918.081
42.0473-1.2697-0.87481.57230.7051.13620.10080.066-0.0955-0.09410.0042-0.1143-0.05760.116-0.1050.0781-0.00670.00970.0920.01710.079530.49816.09712.972
51.1951-0.343-0.73282.4671.50231.8643-0.05720.00460.02170.08760.1121-0.0459-0.00940.1166-0.05490.0785-0.0078-0.03340.06640.02670.049226.0723.46225.424
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 32
2X-RAY DIFFRACTION2A33 - 79
3X-RAY DIFFRACTION3A80 - 110
4X-RAY DIFFRACTION4A111 - 149
5X-RAY DIFFRACTION5A150 - 220

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