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- PDB-1zay: PURINE REPRESSOR-HYPOXANTHINE-MODIFIED-PURF-OPERATOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1zay
TitlePURINE REPRESSOR-HYPOXANTHINE-MODIFIED-PURF-OPERATOR COMPLEX
Components
  • DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*TP*(1AP)P*TP*TP*TP*TP*CP*GP*T)-3')
  • PROTEIN (PURINE REPRESSOR)
KeywordsTRANSCRIPTION/DNA / COMPLEX (DNA-BINDING REGULATION-MODIFIED DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


guanine binding / negative regulation of purine nucleotide biosynthetic process / purine nucleotide biosynthetic process / DNA-binding transcription repressor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / cytosol
Similarity search - Function
Transcription regulator HTH, PurR / Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) ...Transcription regulator HTH, PurR / Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HYPOXANTHINE / DNA / DNA (> 10) / HTH-type transcriptional repressor PurR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZheleznova, E.E. / Brennan, R.G.
CitationJournal: To be Published
Title: The Roles of Exocyclic Groups in the Central Base-Pair Step in Modulating the Affinity of PurR for its Operator
Authors: Zheleznova, E.E. / Brennan, R.G.
History
DepositionDec 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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
M: DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*TP*(1AP)P*TP*TP*TP*TP*CP*GP*T)-3')
A: PROTEIN (PURINE REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4523
Polymers43,3162
Non-polymers1361
Water45025
1
M: DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*TP*(1AP)P*TP*TP*TP*TP*CP*GP*T)-3')
A: PROTEIN (PURINE REPRESSOR)
hetero molecules

M: DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*TP*(1AP)P*TP*TP*TP*TP*CP*GP*T)-3')
A: PROTEIN (PURINE REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9046
Polymers86,6324
Non-polymers2722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)176.449, 95.187, 81.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-811-

HOH

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Components

#1: DNA chain DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*TP*(1AP)P*TP*TP*TP*TP*CP*GP*T)-3')


Mass: 5224.436 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (PURINE REPRESSOR) / PURR


Mass: 38091.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACP7
#3: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→60 Å / Num. obs: 17098 / % possible obs: 88 % / Redundancy: 3 % / Rsym value: 0.071 / Net I/σ(I): 14.2
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2.8 / % possible all: 75

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Processing

Software
NameClassification
TNTrefinement
bioteXdata reduction
bioteXdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PNR

1pnr


Resolution: 2.7→10 Å / Isotropic thermal model: TNT BCORREL / σ(F): 1 / Stereochemistry target values: TNT CDX_PROTGEO
RfactorNum. reflection% reflection
Rwork0.18 --
obs-17098 88 %
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 347 10 25 3034
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.114
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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