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- PDB-1k6i: Crystal structure of Nmra, a negative transcriptional regulator (... -

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Basic information

Entry
Database: PDB / ID: 1k6i
TitleCrystal structure of Nmra, a negative transcriptional regulator (Trigonal form)
ComponentsNmrA
KeywordsTRANSCRIPTION / Rossmann fold transcriptional regulation short chain dehydrogenase reductase
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
Nitrogen metabolite repression protein nmrA / Nitrogen metabolite repression protein nmrA
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsStammers, D.K. / Ren, J. / Leslie, K. / Nichols, C.E. / Lamb, H.K. / Cocklin, S. / Dodds, A. / Hawkins, A.R.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Expression purication and crystallisation of Aspergillus nidulans Nmra- A Negative regulatory protein.
Authors: Nichols, C.E. / Cocklin, S. / Dodds, A. / Ren, J. / Lamb, H. / Hawkins, A.R. / Stammers, D.K.
History
DepositionOct 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE BASED ON SEQUENCE BOTH GENOMIC DNA AND CDNA SHOWED ARG 238 MOST LIKELY THERE IS AN ERROR ... SEQUENCE BASED ON SEQUENCE BOTH GENOMIC DNA AND CDNA SHOWED ARG 238 MOST LIKELY THERE IS AN ERROR IN THE PUBLISHED SEQUENCE OR A SEQUENCE VARIANT IN THE STRAIN USED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NmrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9775
Polymers38,8351
Non-polymers1424
Water6,828379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.800, 76.800, 104.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein NmrA


Mass: 38835.238 Da / Num. of mol.: 1
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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 46.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: potassium chloride, sodium dihydrogen phosphate, potassium dihydrogen phosphate, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9537 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 23, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 29825 / % possible obs: 88.5 % / Observed criterion σ(I): -1.5 / Redundancy: 10.6 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 9.2 / Num. unique all: 1699 / % possible all: 51.6

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.8→18.89 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1679494.7 / Data cutoff high rms absF: 1679494.7 / 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
Rfree0.258 1474 4.9 %RANDOM
Rwork0.209 ---
obs0.209 29822 88.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.836 Å2 / ksol: 0.417096 e/Å3
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20.55 Å20 Å2
2---0.83 Å20 Å2
3---1.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.23 Å
Luzzati d res low-20 Å
Luzzati sigma a0.27 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.8→18.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 4 381 2915
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_mcbond_it4.675
X-RAY DIFFRACTIONc_mcangle_it5.8210
X-RAY DIFFRACTIONc_scbond_it6.916
X-RAY DIFFRACTIONc_scangle_it8.7115
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.363 93 5.5 %
Rwork0.327 1604 -
obs--51.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM

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