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- PDB-1k6j: Crystal structure of Nmra, a negative transcriptional regulator (... -

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Basic information

Entry
Database: PDB / ID: 1k6j
TitleCrystal structure of Nmra, a negative transcriptional regulator (Monoclinic 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 / MOLECULAR REPLACEMENT / 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, 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
DepositionOct 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Database references
Revision 1.4Aug 16, 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_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 BASED ON SEQUENCE BOTH GENOMIC DNA AND CDNA SHOWED ARG 238 ON CHAINS A AND B. MOST LIKELY THERE IS ... BASED ON SEQUENCE BOTH GENOMIC DNA AND CDNA SHOWED ARG 238 ON CHAINS A AND B. 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
B: NmrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9199
Polymers77,6702
Non-polymers2487
Water15,619867
1
A: NmrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9424
Polymers38,8351
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NmrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9775
Polymers38,8351
Non-polymers1424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.800, 64.300, 110.200
Angle α, β, γ (deg.)90.00, 121.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NmrA


Mass: 38835.238 Da / Num. of mol.: 2
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.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 867 / 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: 2.89 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: sodium chloride, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Details: Nichols, C.E., (2001) Acta Crystallogr., Sect.D, 57, 1722.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
118 mg/mlprotein1drop
43.6 M1reservoirNaCl
50.1 MTris1reservoirpH8.0
2ammonium sulfate1drop
3PEG60001drop

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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: 78344 / % possible obs: 95.5 % / Observed criterion σ(I): -1.5 / Redundancy: 5.2 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 1.3 / Num. unique all: 5966 / % possible all: 73.3
Reflection
*PLUS
Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 73.3 % / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.3

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K6I

1k6i


Resolution: 1.8→19.94 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2110594.76 / Data cutoff high rms absF: 2110594.76 / 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
Rfree0.202 3969 5.1 %RANDOM
Rwork0.165 ---
obs0.164 78321 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.3882 Å2 / ksol: 0.400001 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å20 Å2-1.28 Å2
2--4.35 Å20 Å2
3----1.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.19 Å
Luzzati d res low-20 Å
Luzzati sigma a0.19 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5113 0 7 867 5987
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it3.685
X-RAY DIFFRACTIONc_mcangle_it4.938
X-RAY DIFFRACTIONc_scbond_it6.788
X-RAY DIFFRACTIONc_scangle_it8.7612
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.285 5603 -
Rfree-311 5.3 %
obs--72.8 %
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
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0093
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01
X-RAY DIFFRACTIONc_mcbond_it3.685
X-RAY DIFFRACTIONc_scbond_it6.788
X-RAY DIFFRACTIONc_mcangle_it4.938
X-RAY DIFFRACTIONc_scangle_it8.7612
LS refinement shell
*PLUS
% reflection Rfree: 5.3 % / Rfactor Rwork: 0.285

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