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- PDB-4ma0: The crystal structure of phosphoribosylaminoimidazole carboxylase... -

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Basic information

Entry
Database: PDB / ID: 4ma0
TitleThe crystal structure of phosphoribosylaminoimidazole carboxylase ATPase subunit of Francisella tularensis subsp. tularensis SCHU S4 in complex with partially hydrolysed ATP
ComponentsPhosphoribosylaminoimidazole carboxylase, ATPase subunit
KeywordsLYASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / Rudiment single hybrid motif / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 ...Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / Rudiment single hybrid motif / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / N5-carboxyaminoimidazole ribonucleotide synthase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.982 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of phosphoribosylaminoimidazole carboxylase ATPase subunit of Francisella tularensis subsp. tularensis SCHU S4 in complex with partially hydrolysed ATP
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1625
Polymers41,5221
Non-polymers6404
Water3,531196
1
A: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
hetero molecules

A: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,32410
Polymers83,0432
Non-polymers1,2818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5580 Å2
ΔGint-28 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.861, 84.861, 104.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-578-

HOH

21A-609-

HOH

DetailsExperimentally unknown. It is predicted that the chain A and its symmetry related molecule by the operator Y,X,-Z form a dimer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoribosylaminoimidazole carboxylase, ATPase subunit /


Mass: 41521.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT_0897, purK / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: Q5NGE8, phosphoribosylaminoimidazole carboxylase

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Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8M LiCl, 0.1M Tris, 32% (w/v) PEG4000, 15mM ATP, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 9, 2013 / Details: mirror
RadiationMonochromator: SI 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.98→27 Å / Num. all: 26812 / Num. obs: 26812 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 29.5
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1315 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4M9U

4m9u


Resolution: 1.982→26.835 Å / SU ML: 0.24 / σ(F): 1.33 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1324 5.01 %Random
Rwork0.189 ---
all0.1917 26436 --
obs0.1917 26436 97.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.982→26.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 41 196 3031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072882
X-RAY DIFFRACTIONf_angle_d1.0953907
X-RAY DIFFRACTIONf_dihedral_angle_d14.461035
X-RAY DIFFRACTIONf_chiral_restr0.073456
X-RAY DIFFRACTIONf_plane_restr0.004498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9824-2.06180.3231240.26682743X-RAY DIFFRACTION97
2.0618-2.15560.34851300.24522778X-RAY DIFFRACTION99
2.1556-2.26920.29041690.23062760X-RAY DIFFRACTION99
2.2692-2.41120.32331280.22782757X-RAY DIFFRACTION97
2.4112-2.59730.30961500.22322740X-RAY DIFFRACTION97
2.5973-2.85840.24271520.21272782X-RAY DIFFRACTION98
2.8584-3.27140.30221670.19712797X-RAY DIFFRACTION98
3.2714-4.11920.18921670.1592830X-RAY DIFFRACTION99
4.1192-26.83790.1951370.16012925X-RAY DIFFRACTION95
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)
10.90280.9106-0.02231.0754-0.64872.50430.0114-0.15630.08070.1824-0.0241-0.0182-0.8770.36050.00960.4248-0.06410.0070.2151-0.03180.274423.125232.533314.5705
24.2399-0.60690.23032.87640.26895.43250.1498-0.366-0.25050.1403-0.1324-0.1810.47060.6603-0.01930.28150.00970.04680.46390.05670.225823.641915.205540.1322
30.7646-0.25160.00471.03010.31794.49570.0907-0.1445-0.09660.1020.00970.11450.4214-0.2108-0.06120.1682-0.05350.01520.17550.02750.263216.103613.431917.1001
48.5457-0.62711.39773.8561-1.23974.84540.22420.0077-0.9757-0.107-0.25460.01260.90560.2972-0.17120.5580.1307-0.09550.25670.02660.424226.4802-1.07488.8645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 97 )
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 165 )
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 345 )
4X-RAY DIFFRACTION4chain 'A' and (resid 346 through 366 )

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