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- PDB-1nh7: ATP PHOSPHORIBOSYLTRANSFERASE (ATP-PRTASE) FROM MYCOBACTERIUM TUB... -

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Basic information

Entry
Database: PDB / ID: 1nh7
TitleATP PHOSPHORIBOSYLTRANSFERASE (ATP-PRTASE) FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsATP Phosphoribosyltransferase
KeywordsTRANSFERASE / PRTASE / DE NOVO HIS BIOSYNTHESIS / PRPP / PHOSPHORIBOSYLTRANSFERASE / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / AMP binding / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
ATP phosphoribosyltransferase HisG, long form / Histidine biosynthesis HisG, C-terminal / HisG, C-terminal domain / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta ...ATP phosphoribosyltransferase HisG, long form / Histidine biosynthesis HisG, C-terminal / HisG, C-terminal domain / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP phosphoribosyltransferase / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsCho, Y. / Sharma, V. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of ATP Phosphoribosyltransferase from Mycobacterium Tuberculosis
Authors: Cho, Y. / Sharma, V. / Sacchettini, J.C.
History
DepositionDec 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP Phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1897
Polymers32,6841
Non-polymers5056
Water3,117173
1
A: ATP Phosphoribosyltransferase
hetero molecules

A: ATP Phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,37714
Polymers65,3682
Non-polymers1,00912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
Buried area4480 Å2
ΔGint-150 kcal/mol
Surface area25580 Å2
MethodPISA
2
A: ATP Phosphoribosyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)199,13242
Polymers196,1046
Non-polymers3,02836
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
crystal symmetry operation18_654-x+4/3,-x+y+2/3,-z-1/31
Buried area22050 Å2
ΔGint-533 kcal/mol
Surface area68140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.540, 132.540, 110.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein ATP Phosphoribosyltransferase /


Mass: 32684.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RV / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P60759, UniProt: P9WMN1*PLUS, ATP phosphoribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 16 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
20.1 MMES1reservoirpH6.5
31.8 Mmagnesium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 2000
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→32.3 Å / Num. all: 16645 / Num. obs: 16645 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.43 Å / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.7 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.97 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.15

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→27.74 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.873 / SU B: 12.155 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.911 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26117 547 5.3 %RANDOM
Rwork0.19196 ---
obs0.19559 9850 99.97 %-
all-9853 --
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.308 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.7→27.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 26 173 2272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0480.0222131
X-RAY DIFFRACTIONr_angle_refined_deg3.6651.9882900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3563271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.74215371
X-RAY DIFFRACTIONr_chiral_restr0.2490.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021591
X-RAY DIFFRACTIONr_nbd_refined0.3220.3996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.5202
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.540.396
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.8590.532
X-RAY DIFFRACTIONr_mcbond_it1.5511.51359
X-RAY DIFFRACTIONr_mcangle_it2.5722175
X-RAY DIFFRACTIONr_scbond_it5.1173772
X-RAY DIFFRACTIONr_scangle_it7.6164.5725
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 34
Rwork0.186 721
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)
12.3357-0.4921-1.25652.8055-1.2163.79970.0656-0.00860.02190.0390.06090.1208-0.43740.0332-0.12650.1238-0.06680.01340.0368-0.0170.128770.90961.202-0.727
22.11771.00621.19165.11372.42728.0470.13-0.1162-0.18360.25970.2055-0.24180.1180.7909-0.33560.0726-0.0448-0.03880.3114-0.01110.146997.26357.005-13.159
32.946-0.75661.82155.899-2.85615.1944-0.0846-0.23650.06920.30420.12120.1418-0.3323-0.072-0.03660.05370.0106-0.0240.0654-0.04950.116380.05438.3421.446
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 9021 - 110
2X-RAY DIFFRACTION1AA175 - 184195 - 204
3X-RAY DIFFRACTION1AA194 - 211214 - 231
4X-RAY DIFFRACTION1AA280 - 284300 - 304
6X-RAY DIFFRACTION2AA91 - 174111 - 194
8X-RAY DIFFRACTION3AA212 - 234232 - 254
9X-RAY DIFFRACTION3AA236 - 279256 - 299
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 28 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.048
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg3.6
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.97 Å

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