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- PDB-3lf0: Crystal structure of the ATP bound Mycobacterium tuberculosis nit... -

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Basic information

Entry
Database: PDB / ID: 3lf0
TitleCrystal structure of the ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein
ComponentsNitrogen regulatory protein P-II
KeywordsSIGNALING PROTEIN/TRANSCRIPTION / PII protein / GlnK / GlnB / T-loop / 3-10 helix / C-loop / B-loop / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Nucleotide-binding / Transcription / Transcription regulation / SIGNALING PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


biological process involved in interaction with host / regulation of nitrogen utilization / enzyme regulator activity / ADP binding / ATP binding / plasma membrane / cytosol
Similarity search - Function
Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta ...Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShetty, N.D. / Palaninathan, S.K. / Reddy, M.C.M. / Owen, J.L. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Protein Sci. / Year: 2010
Title: Crystal structures of the apo and ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein.
Authors: Shetty, N.D. / Reddy, M.C. / Palaninathan, S.K. / Owen, J.L. / Sacchettini, J.C.
History
DepositionJan 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Nitrogen regulatory protein P-II
B: Nitrogen regulatory protein P-II
C: Nitrogen regulatory protein P-II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9326
Polymers37,4113
Non-polymers1,5223
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-29 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.742, 69.742, 146.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Nitrogen regulatory protein P-II


Mass: 12470.245 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: glnB, MT2987, MTCY338.08c, Rv2919c / Plasmid: pET28TEV / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P64249, UniProt: P9WN31*PLUS
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Imidazole pH 6.0 and 1.0 M Sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97953 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 2.4→62.99 Å / Num. all: 14020 / Num. obs: 14020 / % possible obs: 99.78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.2
Reflection shellResolution: 2.4→2.464 Å / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.02 / % possible all: 97.92

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3bzq

3bzq


Resolution: 2.4→62.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 17.214 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.416 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27246 744 5 %RANDOM
Rwork0.20418 ---
obs0.20752 14020 99.78 %-
all-14020 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.537 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.4→62.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 93 124 2578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222487
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.862.0143392
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3315306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05823.15292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.79815416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9021521
X-RAY DIFFRACTIONr_chiral_restr0.1160.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021766
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21045
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21635
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2129
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7331.51579
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21522505
X-RAY DIFFRACTIONr_scbond_it2.21431031
X-RAY DIFFRACTIONr_scangle_it3.6964.5887
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 54 -
Rwork0.325 982 -
obs--97.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.90381.6034-2.32694.88820.26717.64560.012-0.8634-0.01250.2834-0.141-0.3561-0.01360.76390.1291-0.03170.009-0.01970.1855-0.0462-0.018626.8557-15.319511.0143
24.47621.0621-1.00055.50830.59914.82980.0134-0.5187-0.33320.4996-0.17450.13230.2851-0.01260.16120.00160.02720.07090.20630.00240.01617.9355-18.635913.0092
35.8778-1.5247-3.79382.407-0.78688.94330.24090.3290.2377-0.2946-0.2616-0.1171-0.5604-0.01330.02070.02890.01080.01530.14420.0048-0.078325.2509-10.6541-9.0025
43.2671-0.1537-2.58590.7527-0.0213.77210.12810.38230.1104-0.1518-0.1730.05-0.3149-0.54540.04490.09250.0347-0.00210.1784-0.00080.027422.4116-10.5034-5.7981
57.9961-1.61630.57446.1053-2.83146.7949-0.38530.1476-0.7672-0.2571-0.13330.03730.918-0.3040.51860.0951-0.07530.17190.12-0.11640.120219.6514-29.9802-1.113
64.5381-1.4731-1.56736.9021-4.176611.5913-0.06940.7715-0.0359-0.70250.14660.37840.0727-1.8305-0.0772-0.0364-0.0462-0.04420.367-0.12-0.007712.821-18.4643-8.4251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 59
2X-RAY DIFFRACTION2A60 - 112
3X-RAY DIFFRACTION3B0 - 44
4X-RAY DIFFRACTION4B45 - 112
5X-RAY DIFFRACTION5C0 - 86
6X-RAY DIFFRACTION6C87 - 112

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