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- PDB-2r2v: Sequence Determinants of the Topology of the Lac Repressor Tetram... -

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Basic information

Entry
Database: PDB / ID: 2r2v
TitleSequence Determinants of the Topology of the Lac Repressor Tetrameric Coiled Coil
ComponentsGCN4 leucine zipper
KeywordsDE NOVO PROTEIN / Coiled coils / anti-parallel tetramer / protein design
Function / homologyACETATE ION / CITRIC ACID
Function and homology information
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, J. / Lu, M.
CitationJournal: Biochemistry / Year: 2007
Title: Conformational specificity of the lac repressor coiled-coil tetramerization domain.
Authors: Liu, J. / Zheng, Q. / Deng, Y. / Li, Q. / Kallenbach, N.R. / Lu, M.
History
DepositionAug 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: GCN4 leucine zipper
B: GCN4 leucine zipper
C: GCN4 leucine zipper
D: GCN4 leucine zipper
E: GCN4 leucine zipper
F: GCN4 leucine zipper
G: GCN4 leucine zipper
H: GCN4 leucine zipper
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,07317
Polymers30,9968
Non-polymers1,0769
Water1,78399
1
A: GCN4 leucine zipper
B: GCN4 leucine zipper
C: GCN4 leucine zipper
D: GCN4 leucine zipper
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,19011
Polymers15,4984
Non-polymers6927
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
MethodPISA
2
E: GCN4 leucine zipper
F: GCN4 leucine zipper
G: GCN4 leucine zipper
H: GCN4 leucine zipper
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8826
Polymers15,4984
Non-polymers3842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.696, 51.696, 99.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein/peptide
GCN4 leucine zipper


Mass: 3874.553 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Gene: GCN4, AAS3, ARG9 / Plasmid: pAE4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M sodium citrate, 5% Jeffamine M-600, 0.05M zinc acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.9→51.7 Å / Num. all: 20545 / Num. obs: 20545 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2048 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NRN

2nrn


Resolution: 1.9→51.71 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.028 / SU ML: 0.102
Isotropic thermal model: Isotropic with TLS group assigned for each peptide chain.
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.169 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24028 1054 5.1 %RANDOM
Rwork0.19108 ---
all0.19347 20545 --
obs0.19347 20545 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.479 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.63 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.9→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 66 99 2210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222110
X-RAY DIFFRACTIONr_angle_refined_deg1.0882.0332814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3095251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66225.77890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25915443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.051511
X-RAY DIFFRACTIONr_chiral_restr0.0620.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021495
X-RAY DIFFRACTIONr_nbd_refined0.1970.21025
X-RAY DIFFRACTIONr_nbtor_refined0.2830.21455
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2105
X-RAY DIFFRACTIONr_metal_ion_refined0.0280.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.219
X-RAY DIFFRACTIONr_mcbond_it0.5361.51327
X-RAY DIFFRACTIONr_mcangle_it0.9222023
X-RAY DIFFRACTIONr_scbond_it1.6993850
X-RAY DIFFRACTIONr_scangle_it2.6644.5791
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 86 -
Rwork0.214 1399 -
obs-1485 99.87 %
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)
13.0526-1.1622-0.17298.4863-8.309124.9146-0.10370.1652-0.1627-0.09350.14520.534-0.0093-0.95-0.0415-0.2665-0.0192-0.036-0.1998-0.0482-0.1097-27.607-10.019-8.562
24.3466-2.54824.60147.2173-5.374621.27550.13710.0363-0.0176-0.14680.16990.7230.3819-0.9266-0.307-0.22240.0163-0.0007-0.1596-0.0353-0.0435-29.785-1.176-4.229
34.9001-2.57233.35587.6723-3.816210.21580.05680.06810.15930.0241-0.09690.00980.00570.09130.0401-0.2290.008-0.0102-0.257-0.0613-0.1768-20.663-0.303-2.425
42.6957-0.1244-0.58686.855-5.595111.98990.08810.0641-0.00520.0142-0.0564-0.0165-0.22140.1937-0.0317-0.25410.0141-0.0157-0.2281-0.0568-0.1832-19.379-8.33-8.249
518.9477-5.76061.24117.18551.46054.01340.12730.1272-0.80790.1192-0.01330.3140.1322-0.0667-0.114-0.1574-0.0102-0.0283-0.2413-0.032-0.1882-12.71710.40412.505
612.1503-7.41320.452913.08743.04535.0571-0.5611-0.74220.30510.85560.8167-0.51210.41370.2385-0.2556-0.110.0549-0.0657-0.1818-0.1044-0.152-15.3683.16.532
717.1523-12.9908-1.324219.46134.63565.2384-0.2136-0.05450.6575-0.01770.3649-0.9109-0.26360.1728-0.1513-0.1625-0.0481-0.0588-0.2179-0.0238-0.1743-13.7557.605-0.489
816.4944-4.47751.06078.87332.04094.37890.5041.4343-0.6349-0.4676-0.2165-0.2921-0.08580.455-0.2876-0.16950.0057-0.0485-0.0439-0.0787-0.1896-7.56613.7694.917
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 342 - 34
2X-RAY DIFFRACTION2BB1 - 331 - 33
3X-RAY DIFFRACTION3CC1 - 331 - 33
4X-RAY DIFFRACTION4DD2 - 342 - 34
5X-RAY DIFFRACTION5EE1 - 311 - 31
6X-RAY DIFFRACTION6FF3 - 343 - 34
7X-RAY DIFFRACTION7GG1 - 331 - 33
8X-RAY DIFFRACTION8HH3 - 333 - 33

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