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- PDB-5u99: Transition state analysis of adenosine triphosphate phosphoribosy... -

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Basic information

Entry
Database: PDB / ID: 5u99
TitleTransition state analysis of adenosine triphosphate phosphoribosyltransferase
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / ATP-PRT / HisG / Adenosine triphosphate phosphoribosyltransferase
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
ADENOSINE-5'-TRIPHOSPHATE / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMoggre, G.-J. / Poulin, M.B. / Tyler, P.C. / Schramm, V.L. / Parker, E.J.
Funding support New Zealand, 3items
OrganizationGrant numberCountry
Maurice Wilkins centre Fund New Zealand
UoC Doctoral Scholarship New Zealand
IRL Sir Roy McKenzie Trust New Zealand
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Transition State Analysis of Adenosine Triphosphate Phosphoribosyltransferase.
Authors: Moggre, G.J. / Poulin, M.B. / Tyler, P.C. / Schramm, V.L. / Parker, E.J.
History
DepositionDec 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Feb 26, 2020Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.3Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)31,4857
Polymers30,6411
Non-polymers8446
Water50428
1
A: ATP phosphoribosyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)188,90942
Polymers183,8456
Non-polymers5,06436
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_554y,x,-z-11
crystal symmetry operation5_554x-y,-y,-z-11
crystal symmetry operation6_554-x,-x+y,-z-11
Buried area24810 Å2
ΔGint-504 kcal/mol
Surface area64760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.758, 134.758, 111.005
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-305-

MG

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Components

#1: Protein ATP phosphoribosyltransferase / ATP-PRTase


Mass: 30640.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: hisG, Rv2121c, MTCY261.17c / Cell line (production host): BL21 star / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): pLysS / References: UniProt: P9WMN1, ATP phosphoribosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.16 Å3/Da / Density % sol: 61.09 % / Description: Crystals grew as medium sizes prisms overnight
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M magnesium sulphate and 0.1 M, 2-(N-morpholino)ethanesulfonic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→80.43 Å / Num. obs: 15289 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.773 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.492 / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB:1NH7

1nh7


Resolution: 2.4→80.43 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.934 / SU B: 16.133 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.308 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25051 747 4.9 %RANDOM
Rwork0.21571 ---
obs0.21749 14540 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.545 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20.82 Å2-0 Å2
2--1.64 Å2-0 Å2
3----5.33 Å2
Refinement stepCycle: 1 / Resolution: 2.4→80.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 48 28 2057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192096
X-RAY DIFFRACTIONr_bond_other_d0.0020.021924
X-RAY DIFFRACTIONr_angle_refined_deg1.5192.0032873
X-RAY DIFFRACTIONr_angle_other_deg0.95834400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9295279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.63723.37874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88115288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0341515
X-RAY DIFFRACTIONr_chiral_restr0.080.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1413.5861122
X-RAY DIFFRACTIONr_mcbond_other1.1413.5851121
X-RAY DIFFRACTIONr_mcangle_it1.985.3731399
X-RAY DIFFRACTIONr_mcangle_other1.9795.3751400
X-RAY DIFFRACTIONr_scbond_it1.3033.761973
X-RAY DIFFRACTIONr_scbond_other1.3023.761974
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0635.6151475
X-RAY DIFFRACTIONr_long_range_B_refined4.40142.8112153
X-RAY DIFFRACTIONr_long_range_B_other4.38942.7852151
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 61 -
Rwork0.317 1069 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -21.69 Å / Origin y: 4.5235 Å / Origin z: -36.1812 Å
111213212223313233
T0.0876 Å20.0031 Å20.0901 Å2-0.1263 Å2-0.0047 Å2--0.1406 Å2
L1.4725 °20.0761 °20.7157 °2-1.1684 °20.1385 °2--1.6532 °2
S0.1187 Å °-0.2718 Å °-0.0119 Å °0.1218 Å °0.007 Å °0.1194 Å °-0.1513 Å °-0.2673 Å °-0.1257 Å °

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