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- PDB-1k6x: Crystal structure of Nmra, a negative transcriptional regulator i... -

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Basic information

Entry
Database: PDB / ID: 1k6x
TitleCrystal structure of Nmra, a negative transcriptional regulator in complex with NAD at 1.5 A resolution (Trigonal form)
ComponentsNmrA
KeywordsTRANSCRIPTION / Rossmann fold transcriptional regulation short chain dehydrogenase reductase NADH binding
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nitrogen metabolite repression protein nmrA / Nitrogen metabolite repression protein nmrA
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: 2002
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 crystallisation 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 17, 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 1.3Nov 16, 2011Group: Atomic model
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 999SEQUENCE 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 AS PER AUTHOR

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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)39,7118
Polymers38,8351
Non-polymers8767
Water10,791599
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.690, 76.690, 104.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1055-

HOH

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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.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
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
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 M1reservoirKCl
50.1 MMES1reservoirpH6.5
60.1 Msodium potassium phosphate1reservoir
2ammonium sulfate1drop
3PEG60001drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9919 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 54613 / % possible obs: 95 % / Observed criterion σ(I): -1.5 / Redundancy: 8.6 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 29.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3872 / % possible all: 68.4
Reflection shell
*PLUS
% possible obs: 68.4 % / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.2

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Processing

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

1k6i


Resolution: 1.5→28.03 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1612646.17 / Data cutoff high rms absF: 1612646.17 / 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
Rfree0.222 2766 5.2 %RANDOM
Rwork0.189 ---
obs0.179 54579 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 78.6435 Å2 / ksol: 0.382178 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å2-0.9 Å20 Å2
2---1.43 Å20 Å2
3---2.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-30 Å
Luzzati sigma a0.18 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.5→28.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 50 599 3213
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_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it3.346
X-RAY DIFFRACTIONc_mcangle_it4.2510
X-RAY DIFFRACTIONc_scbond_it6.168
X-RAY DIFFRACTIONc_scangle_it7.7516
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.346 200 5.2 %
Rwork0.333 3671 -
obs--68.4 %
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
X-RAY DIFFRACTION5NAD.PAR
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5.2 % / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0091
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
X-RAY DIFFRACTIONc_mcbond_it3.346
X-RAY DIFFRACTIONc_scbond_it6.168
X-RAY DIFFRACTIONc_mcangle_it4.2510
X-RAY DIFFRACTIONc_scangle_it7.7516
LS refinement shell
*PLUS
Rfactor Rfree: 0.346 / Rfactor Rwork: 0.333

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