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- PDB-1vch: Crystal Structure of a Phosphoribosyltransferase-related protein ... -

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Basic information

Entry
Database: PDB / ID: 1vch
TitleCrystal Structure of a Phosphoribosyltransferase-related protein from Thermus thermophilus
ComponentsPhosphoribosyltransferase-related protein
KeywordsTRANSFERASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


nucleoside metabolic process / glycosyltransferase activity
Similarity search - Function
Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Putative adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MAD / Resolution: 1.94 Å
AuthorsRehse, P.H. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of a Phosphoribosyltransferase-related protein from Thermus thermophilus
Authors: Rehse, P.H. / Tahirov, T.H.
History
DepositionMar 8, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_label_seq_id / _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_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosyltransferase-related protein
B: Phosphoribosyltransferase-related protein
C: Phosphoribosyltransferase-related protein
D: Phosphoribosyltransferase-related protein
E: Phosphoribosyltransferase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,24115
Polymers96,7835
Non-polymers45810
Water6,720373
1
A: Phosphoribosyltransferase-related protein
B: Phosphoribosyltransferase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9046
Polymers38,7132
Non-polymers1914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-32 kcal/mol
Surface area14980 Å2
MethodPISA
2
C: Phosphoribosyltransferase-related protein
D: Phosphoribosyltransferase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9447
Polymers38,7132
Non-polymers2315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-37 kcal/mol
Surface area15060 Å2
MethodPISA
3
E: Phosphoribosyltransferase-related protein
hetero molecules

E: Phosphoribosyltransferase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7844
Polymers38,7132
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
4
C: Phosphoribosyltransferase-related protein
D: Phosphoribosyltransferase-related protein
hetero molecules

C: Phosphoribosyltransferase-related protein
D: Phosphoribosyltransferase-related protein
hetero molecules

A: Phosphoribosyltransferase-related protein
B: Phosphoribosyltransferase-related protein
E: Phosphoribosyltransferase-related protein
hetero molecules

A: Phosphoribosyltransferase-related protein
B: Phosphoribosyltransferase-related protein
E: Phosphoribosyltransferase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,48230
Polymers193,56710
Non-polymers91520
Water18010
TypeNameSymmetry operationNumber
crystal symmetry operation3_546x+1/2,y-1/2,z+11
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area21050 Å2
ΔGint-162 kcal/mol
Surface area69860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.419, 61.405, 102.389
Angle α, β, γ (deg.)90.00, 93.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-1006-

HOH

DetailsThe biological unit is a dimer. Chains A and B compose one, chains C and D a second, and chain E related to itself (crystallographic C2) composes the third.

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Components

#1: Protein
Phosphoribosyltransferase-related protein


Mass: 19356.676 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q5SHW7, adenine phosphoribosyltransferase
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.72 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: MES, PEG 10K, CaAc, MeOH, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 / Wavelength: 0.976, 0.97935, 0.982, 0.97904, 0.973
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 4, 2003 / Details: mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si111SINGLE WAVELENGTHMx-ray1
2Si111MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9761
30.979351
40.9821
50.979041
60.9731
ReflectionResolution: 1.9→50 Å / Num. all: 80673 / Num. obs: 80673 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.1 / Num. unique all: 7693 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MAD
Starting model: Partial structure from MAD data set

Resolution: 1.94→44.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1594001.24 / 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
Rfree0.259 3728 5 %RANDOM
Rwork0.232 ---
obs0.232 73828 95.8 %-
all-73828 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.8369 Å2 / ksol: 0.338478 e/Å3
Displacement parametersBiso mean: 46.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å23.61 Å2
2---0.3 Å20 Å2
3----0.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.94→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6504 0 6 389 6899
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it3.931.5
X-RAY DIFFRACTIONc_mcangle_it5.142
X-RAY DIFFRACTIONc_scbond_it5.392
X-RAY DIFFRACTIONc_scangle_it7.022.5
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 587 5 %
Rwork0.288 11038 -
obs--91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ACY.PARAMACY.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM

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