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- PDB-1xgk: CRYSTAL STRUCTURE OF N12G AND A18G MUTANT NMRA -

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Basic information

Entry
Database: PDB / ID: 1xgk
TitleCRYSTAL STRUCTURE OF N12G AND A18G MUTANT NMRA
ComponentsNITROGEN METABOLITE REPRESSION REGULATOR NMRA
KeywordsTRANSCRIPTION / ROSSMANN FOLD / TRANSCRIPTIONAL REGULATION / SHORT CHAIN DEHYDROGENASE / REDUCTASE / NADP BINDING / NMRA
Function / homology
Function and homology information


nitrogen catabolite repression of transcription from RNA polymerase II promoter / nitrogen catabolite repression of transcription / regulation of nitrogen utilization / NADP+ binding / NAD+ binding / NAD binding / oxidoreductase activity / negative regulation of DNA-templated transcription / nucleus / cytoplasm
Similarity search - Function
: / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Nitrogen metabolite repression protein nmrA / Nitrogen metabolite repression protein nmrA
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLamb, H.K. / Ren, J. / Park, A. / Johnson, C. / Leslie, K. / Cocklin, S. / Thompson, P. / Mee, C. / Cooper, A. / Stammers, D.K. / Hawkins, A.R.
Citation
Journal: Protein Sci. / Year: 2004
Title: Modulation of the ligand binding properties of the transcription repressor NmrA by GATA-containing DNA and site-directed mutagenesis
Authors: Lamb, H.K. / Ren, J. / Park, A. / Johnson, C. / Leslie, K. / Cocklin, S. / Thompson, P. / Mee, C. / Cooper, A. / Stammers, D.K. / Hawkins, A.R.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: The Negative Transcriptional Regulator Nmra Discriminates between Oxidized and Reduced Dinucleotides
Authors: Lamb, H.K. / Leslie, K. / Dodds, A.L. / Nutley, M. / Cooper, A. / Johnson, C. / Thompson, P. / Stammers, D.K. / Hawkins, A.R.
#2: Journal: Embo J. / Year: 2001
Title: The Structure of the Negative Transcriptional Regulator Nmra Reveals a Structural Superfamily which Includes the Short-Chain Dehydrogenase/Reductases
Authors: Stammers, D.K. / Ren, J. / Leslie, K. / Nichols, C.E. / Lamb, H.K. / Cocklin, S. / Dodds, A. / Hawkins, A.R.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Expression, Purification and Crystallization of Aspergillus Nidulans Nmra, a Negative Regulatory Protein Involved in Nitrogen-Metabolite Repression
Authors: Nichols, C.E. / Cocklin, S. / Dodds, A. / Ren, J. / Lamb, H. / Hawkins, A.R. / Stammers, D.K.
History
DepositionSep 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,28512
Polymers38,7641
Non-polymers52111
Water10,683593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.610, 76.610, 103.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NITROGEN METABOLITE REPRESSION REGULATOR NMRA


Mass: 38764.164 Da / Num. of mol.: 1 / Mutation: N12G, A18G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Gene: NMRA / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): BL23 DE3 / References: UniProt: O59919, UniProt: Q5AU62*PLUS

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Non-polymers , 5 types, 604 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#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.: 593 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: KCL, K/NA DIHYDROGEN PHOSPHATE,TRIS, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9323 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9323 Å / Relative weight: 1
ReflectionResolution: 1.4→25 Å / Num. obs: 69599 / % possible obs: 99.6 % / Observed criterion σ(I): -1.5 / Redundancy: 9.3 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 36.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6649 / % possible all: 96.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1k6i

1k6i


Resolution: 1.4→24.38 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1744021.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3534 5.1 %RANDOM
Rwork0.193 ---
obs0.193 69565 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.0789 Å2 / ksol: 0.371527 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å2-0.68 Å20 Å2
2---1.96 Å20 Å2
3---3.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.4→24.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 20 593 3183
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it3.474
X-RAY DIFFRACTIONc_mcangle_it4.578
X-RAY DIFFRACTIONc_scbond_it5.548
X-RAY DIFFRACTIONc_scangle_it7.2516
LS refinement shellResolution: 1.4→1.45 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.313 350 5.3 %
Rwork0.325 6293 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER_REP.TOP

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