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- PDB-7dam: Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 7dam
TitleAdenosine triphosphate phosphoribosyltransferase from Vibrio cholerae
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / Adenosine triphosphate phosphoribosyltransferase
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / magnesium ion binding / ATP binding / 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. / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal
Similarity search - Domain/homology
ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsPal, R.K. / Gourinath, S. / Biswal, B.K.
CitationJournal: To Be Published
Title: Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae
Authors: Pal, R.K. / Gourinath, S. / Biswal, B.K.
History
DepositionOct 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP phosphoribosyltransferase
B: ATP phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)69,1582
Polymers69,1582
Non-polymers00
Water18010
1
A: ATP phosphoribosyltransferase
B: ATP phosphoribosyltransferase

A: ATP phosphoribosyltransferase
B: ATP phosphoribosyltransferase

A: ATP phosphoribosyltransferase
B: ATP phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)207,4756
Polymers207,4756
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area12610 Å2
ΔGint-101 kcal/mol
Surface area77650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.512, 117.512, 121.339
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 10 - 303 / Label seq-ID: 16 - 309

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein ATP phosphoribosyltransferase / ATP-PRTase


Mass: 34579.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain M66-2) (bacteria)
Strain: M66-2 / Gene: hisG, VCM66_1088 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3LU29, ATP phosphoribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.1 M Sodium acetate trihydrate pH 4.6 2.0 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.543
11K, H, -L20.457
ReflectionResolution: 2.7→50 Å / Num. obs: 17005 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC1/2: 0.995 / Net I/σ(I): 14.54
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 1706 / CC1/2: 0.451

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H3D

1h3d


Resolution: 2.7→36.67 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.724 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.534 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 1745 10.3 %RANDOM
Rwork0.2103 ---
obs0.2158 15259 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.49 Å2 / Biso mean: 58.298 Å2 / Biso min: 38.28 Å2
Baniso -1Baniso -2Baniso -3
1-11.86 Å20 Å20 Å2
2--11.86 Å20 Å2
3----23.73 Å2
Refinement stepCycle: final / Resolution: 2.7→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 0 10 3758
Biso mean---56.7 -
Num. residues----556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133782
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173445
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.6275163
X-RAY DIFFRACTIONr_angle_other_deg1.2141.5737840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9355548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58224.113124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.71215521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0151513
X-RAY DIFFRACTIONr_chiral_restr0.0490.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02680
Refine LS restraints NCS

Ens-ID: 1 / Number: 6192 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.705→2.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 112 -
Rwork0.27 1136 -
all-1248 -
obs--99.84 %

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