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- PDB-4m9u: The crystal structure of phosphoribosylaminoimidazole carboxylase... -

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Basic information

Entry
Database: PDB / ID: 4m9u
TitleThe crystal structure of phosphoribosylaminoimidazole carboxylase ATPase subunit of Francisella tularensis subsp. tularensis SCHU S4
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
ACETATE ION / FORMIC ACID / N5-carboxyaminoimidazole ribonucleotide synthase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.599 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
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

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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)42,11015
Polymers41,3921
Non-polymers71814
Water5,549308
1
A: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
hetero molecules

A: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,22130
Polymers82,7852
Non-polymers1,43628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8200 Å2
ΔGint-86 kcal/mol
Surface area28510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.313, 85.313, 107.673
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-501-

HOH

21A-568-

HOH

31A-705-

HOH

DetailsExperimentally unknown. It is predicted that the chainA and its symmtry-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: 41392.449 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, 322 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.8M Sodium Acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 2, 2013 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.599→36 Å / Num. all: 53157 / Num. obs: 53157 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 9.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 44.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2601 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.599→35.962 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 17.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 2700 5.09 %random
Rwork0.1661 ---
all0.1676 53070 --
obs0.1676 53070 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.599→35.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 46 308 3150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062904
X-RAY DIFFRACTIONf_angle_d1.0873928
X-RAY DIFFRACTIONf_dihedral_angle_d13.0131050
X-RAY DIFFRACTIONf_chiral_restr0.076459
X-RAY DIFFRACTIONf_plane_restr0.004511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.599-1.62810.21681290.19842572X-RAY DIFFRACTION99
1.6281-1.65940.27371280.20562636X-RAY DIFFRACTION100
1.6594-1.69330.20481560.18532593X-RAY DIFFRACTION100
1.6933-1.73010.22711550.17692581X-RAY DIFFRACTION100
1.7301-1.77030.18761560.17772625X-RAY DIFFRACTION100
1.7703-1.81460.2041390.17422621X-RAY DIFFRACTION100
1.8146-1.86370.18771290.1752612X-RAY DIFFRACTION100
1.8637-1.91850.19671440.16692612X-RAY DIFFRACTION100
1.9185-1.98040.21261340.15722634X-RAY DIFFRACTION100
1.9804-2.05120.1871280.15282661X-RAY DIFFRACTION100
2.0512-2.13330.1521390.14822631X-RAY DIFFRACTION100
2.1333-2.23040.17051350.14692642X-RAY DIFFRACTION100
2.2304-2.3480.20371530.15632635X-RAY DIFFRACTION100
2.348-2.4950.19351390.16782655X-RAY DIFFRACTION100
2.495-2.68760.20591420.18432671X-RAY DIFFRACTION100
2.6876-2.9580.2061450.18042670X-RAY DIFFRACTION100
2.958-3.38570.19451550.16982699X-RAY DIFFRACTION100
3.3857-4.26460.16551400.14042740X-RAY DIFFRACTION100
4.2646-35.97130.21541540.17672880X-RAY DIFFRACTION100
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)
10.87930.32940.63390.64230.45291.08640.0502-0.1472-0.0770.1043-0.0156-0.00870.147-0.0897-0.0330.1143-0.00470.00750.12930.01250.117321.574511.819116.8838
22.1687-0.1333-0.73911.1171-0.78011.6309-0.0733-0.27070.34560.20560.19610.1879-0.438-0.4977-0.11040.31170.133-0.02560.4432-0.02910.210317.486128.261341.9514
30.8068-0.28910.37480.5622-0.10141.1533-0.0864-0.10750.17540.09230.0304-0.0716-0.2116-0.01720.04340.1191-0.0136-0.01280.112-0.03350.129226.372231.340916.4184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 165 )
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 365 )

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