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- PDB-7dah: Adenosine triphosphate phosphoribosyltransferase from Vibrio chol... -

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Basic information

Entry
Database: PDB / ID: 7dah
TitleAdenosine triphosphate phosphoribosyltransferase from Vibrio cholerae in complex with ATP and PRPP
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / ATP / PRPP
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
ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Chem-PRP / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.92 Å
AuthorsPal, R.K. / Gourinath, S. / Biswal, B.K.
CitationJournal: To Be Published
Title: Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae in complex with ATP and PRPP
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
C: ATP phosphoribosyltransferase
D: ATP phosphoribosyltransferase
E: ATP phosphoribosyltransferase
F: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,40126
Polymers207,4756
Non-polymers2,92620
Water3,585199
1
A: ATP phosphoribosyltransferase
C: ATP phosphoribosyltransferase
D: ATP phosphoribosyltransferase
F: ATP phosphoribosyltransferase
hetero molecules

B: ATP phosphoribosyltransferase

E: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,40126
Polymers207,4756
Non-polymers2,92620
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
crystal symmetry operation3_665-x+y+1,-x+1,z+1/31
Buried area23000 Å2
ΔGint-140 kcal/mol
Surface area74840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.603, 136.603, 121.931
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNMETMETAA10 - 30316 - 309
21GLNGLNMETMETBB10 - 30316 - 309
12THRTHRGLUGLUAA9 - 30415 - 310
22THRTHRGLUGLUCC9 - 30415 - 310
13THRTHRGLUGLUAA9 - 30415 - 310
23THRTHRGLUGLUDD9 - 30415 - 310
14GLNGLNGLUGLUAA10 - 30416 - 310
24GLNGLNGLUGLUEE10 - 30416 - 310
15THRTHRGLUGLUAA9 - 30415 - 310
25THRTHRGLUGLUFF9 - 30415 - 310
16GLNGLNMETMETBB10 - 30316 - 309
26GLNGLNMETMETCC10 - 30316 - 309
17GLNGLNMETMETBB10 - 30316 - 309
27GLNGLNMETMETDD10 - 30316 - 309
18GLNGLNMETMETBB10 - 30316 - 309
28GLNGLNMETMETEE10 - 30316 - 309
19GLNGLNMETMETBB10 - 30316 - 309
29GLNGLNMETMETFF10 - 30316 - 309
110THRTHRGLUGLUCC9 - 30415 - 310
210THRTHRGLUGLUDD9 - 30415 - 310
111GLNGLNGLUGLUCC10 - 30416 - 310
211GLNGLNGLUGLUEE10 - 30416 - 310
112THRTHRGLUGLUCC9 - 30415 - 310
212THRTHRGLUGLUFF9 - 30415 - 310
113GLNGLNGLUGLUDD10 - 30416 - 310
213GLNGLNGLUGLUEE10 - 30416 - 310
114THRTHRGLUGLUDD9 - 30415 - 310
214THRTHRGLUGLUFF9 - 30415 - 310
115GLNGLNGLUGLUEE10 - 30416 - 310
215GLNGLNGLUGLUFF10 - 30416 - 310

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein / Sugars , 2 types, 8 molecules ABCDEF

#1: Protein
ATP phosphoribosyltransferase / ATP-PRTase


Mass: 34579.195 Da / Num. of mol.: 6
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
#8: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O14P3 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 7 types, 217 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.1M Morpheus Amino acids , 0.1M Morpheus Buffer System 3 , 30 % v/v Morpheus Precipitant Mix 3 (condition H11 of Morpheus screen from Molecular Dimensions)

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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: Jul 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.92→35 Å / Num. obs: 55130 / % possible obs: 99.7 % / Redundancy: 5.3 % / CC1/2: 0.992 / Net I/σ(I): 13
Reflection shellResolution: 2.92→3.02 Å / Num. unique obs: 5579 / CC1/2: 0.497

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H3D

1h3d


Resolution: 2.92→28.32 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.892 / SU B: 41.978 / SU ML: 0.336 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 2553 4.6 %RANDOM
Rwork0.2163 ---
obs0.2186 52562 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: 202.17 Å2 / Biso mean: 64.28 Å2 / Biso min: 25.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20.58 Å20 Å2
2--1.17 Å20 Å2
3----3.79 Å2
Refinement stepCycle: final / Resolution: 2.92→28.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12785 0 176 199 13160
Biso mean--111.7 50.87 -
Num. residues----1735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01313090
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712453
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.64417690
X-RAY DIFFRACTIONr_angle_other_deg1.3291.57428699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5351715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76822.368549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.649152242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8731583
X-RAY DIFFRACTIONr_chiral_restr0.0760.21822
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214486
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022476
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A75180.13
12B75180.13
21A77820.11
22C77820.11
31A82230.08
32D82230.08
41A74570.13
42E74570.13
51A76290.12
52F76290.12
61B74560.13
62C74560.13
71B75050.13
72D75050.13
81B79180.09
82E79180.09
91B74100.13
92F74100.13
101C77580.12
102D77580.12
111C74080.12
112E74080.12
121C80080.09
122F80080.09
131D74990.12
132E74990.12
141D76040.12
142F76040.12
151E73300.12
152F73300.12
LS refinement shellResolution: 2.92→2.995 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.418 176 -
Rwork0.34 3896 -
obs--99.08 %
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)
10.6722-0.52680.41120.9403-0.29990.3183-0.0899-0.0052-0.04610.01340.05770.0158-0.03090.12760.03220.10080.03080.20410.26250.05920.47811.168249.0843.0772
20.4046-0.53910.21010.7414-0.3640.56260.0584-0.0964-0.30520.02730.14130.4758-0.23810.1445-0.19970.1826-0.07280.14810.15080.17740.6561-20.36355.17410.4455
30.09870.1055-0.14950.6374-0.11190.84390.05970.02730.0559-0.0090.04710.47890.08650.2148-0.10680.10360.0530.02020.1536-0.04050.58021.584948.2811-34.8633
41.1416-0.36980.4480.1791-0.23120.30940.01430.0655-0.07040.0788-0.01810.029-0.1297-0.02010.00370.19130.06530.05670.1684-0.20160.506937.080233.9716-44.5257
51.257-0.16170.450.0257-0.03190.62520.11510.0652-0.5464-0.02450.04030.0332-0.25060.1162-0.15540.1805-0.0378-0.07810.1084-0.21480.652658.028710.0664-41.8837
60.35510.23550.00350.24490.04940.76380.0331-0.0157-0.37760.03460.0776-0.2733-0.1208-0.1932-0.11070.1030.050.03650.1606-0.01630.580441.105225.5478-6.6993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 304
2X-RAY DIFFRACTION2B10 - 303
3X-RAY DIFFRACTION3C9 - 304
4X-RAY DIFFRACTION4D9 - 304
5X-RAY DIFFRACTION5E10 - 304
6X-RAY DIFFRACTION6F8 - 304

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