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- PDB-1zme: CRYSTAL STRUCTURE OF PUT3/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1zme
TitleCRYSTAL STRUCTURE OF PUT3/DNA COMPLEX
Components
  • DNA (5'-D(*AP*CP*GP*GP*AP*GP*(5IU)P*TP*GP*GP*CP*TP*(5IU)P*CP*CP*CP*G)-3')
  • DNA (5'-D(*AP*CP*GP*GP*GP*AP*AP*GP*CP*CP*AP*AP*CP*TP*CP*CP*G)-3')
  • PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR
KeywordsTRANSCRIPTION/DNA / COMPLEX (TRANSCRIPTION REGULATION-DNA) / PUT3 / ZN2CYS6 / BINUCLEAR CLUSTER / TRANSCRIPTION FACTOR / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of proline catabolic process to glutamate / proline metabolic process / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / Single helix bin / CD2-Gal4 / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. ...Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / Single helix bin / CD2-Gal4 / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Basic-leucine zipper domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Few Secondary Structures / Irregular / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Proline utilization trans-activator
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsSwaminathan, K. / Marmorstein, R.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster.
Authors: Swaminathan, K. / Flynn, P. / Reece, R.J. / Marmorstein, R.
History
DepositionAug 6, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*GP*GP*GP*AP*AP*GP*CP*CP*AP*AP*CP*TP*CP*CP*G)-3')
B: DNA (5'-D(*AP*CP*GP*GP*AP*GP*(5IU)P*TP*GP*GP*CP*TP*(5IU)P*CP*CP*CP*G)-3')
C: PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR
D: PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8388
Polymers26,5764
Non-polymers2624
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.650, 121.650, 39.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Cell settinghexagonal
Space group name H-MP6

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Components

#1: DNA chain DNA (5'-D(*AP*CP*GP*GP*GP*AP*AP*GP*CP*CP*AP*AP*CP*TP*CP*CP*G)-3')


Mass: 5206.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene (production host): PUT3 (31-100) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LYS-S
#2: DNA chain DNA (5'-D(*AP*CP*GP*GP*AP*GP*(5IU)P*TP*GP*GP*CP*TP*(5IU)P*CP*CP*CP*G)-3')


Mass: 5443.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Protein PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR / PUT3 (PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR)


Mass: 7963.330 Da / Num. of mol.: 2 / Fragment: RESIDUES 31 - 100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P25502
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.0 MM DIMER PROTEIN + 1.5 MM DNA DUPLEX PREPARED. 1.0 MILLILITER (0.1 M MES BUFFER, PH 6.5 + 10 MM MG CL2 + 20 MM NA CL + 20 % PEG 4K) RESERVOIR. HANGING DROP, LINBRO BOX, 20 DEGREE C. ...Details: 1.0 MM DIMER PROTEIN + 1.5 MM DNA DUPLEX PREPARED. 1.0 MILLILITER (0.1 M MES BUFFER, PH 6.5 + 10 MM MG CL2 + 20 MM NA CL + 20 % PEG 4K) RESERVOIR. HANGING DROP, LINBRO BOX, 20 DEGREE C. WITHIN 5 DAYS, 0.2 X 0.3 X 0.4 MM CRYSTALS., vapor diffusion - hanging drop, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES BUFFER11
2MGCL211
3NACL11
4PEG 400011
5MES BUFFER12
6MGCL212
7NACL12
8PEG 400012

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 2, 1996 / Details: MSC/YALE MIRRORS
RadiationMonochromator: MSC YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 11024 / % possible obs: 95 % / Redundancy: 2.9 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.078

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MIR / Resolution: 2.5→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1057 10.2 %RANDOM
Rwork0.208 ---
obs0.208 10388 91.5 %-
Displacement parametersBiso mean: 24.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 690 6 157 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.753
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.631.5
X-RAY DIFFRACTIONx_mcangle_it3.992
X-RAY DIFFRACTIONx_scbond_it4.322
X-RAY DIFFRACTIONx_scangle_it6.032.5
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 137 9.6 %
Rwork0.324 1295 -
obs--76.5 %

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