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- PDB-4ma5: The crystal structure of phosphoribosylaminoimidazole carboxylase... -

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Basic information

Entry
Database: PDB / ID: 4ma5
TitleThe crystal structure of phosphoribosylaminoimidazole carboxylase ATPase subunit of Francisella tularensis subsp. tularensis SCHU S4 in complex with an ATP analog, AMP-PNP.
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 / : / Ribonucleotide synthetase preATP-grasp domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / Rudiment single hybrid motif ...Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / : / Ribonucleotide synthetase preATP-grasp domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / Rudiment single hybrid motif / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / FORMIC ACID / N5-carboxyaminoimidazole ribonucleotide synthase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.809 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 an ATP analog, AMP-PNP.
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 25, 2013Group: Structure summary
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Sep 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 / 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.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)41,2896
Polymers40,5991
Non-polymers6905
Water4,288238
1
A: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
hetero molecules

A: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,57812
Polymers81,1972
Non-polymers1,38110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6240 Å2
ΔGint-55 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.943, 84.943, 106.539
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-618-

HOH

21A-630-

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: 40598.590 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, 243 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M (NH4)2SO4, 0.1M NaAct, 25% (w/v) PEG 4000, 15mM AMP-PNP, pH 4.6, 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: 0.9786 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: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.809→27 Å / Num. all: 34710 / Num. obs: 34710 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 6.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 40.1
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 6 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.85 / Num. unique all: 1753 / % possible all: 97.9

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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: 1.809→26.861 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 1730 4.99 %Random
Rwork0.1729 ---
all0.1751 34667 --
obs0.1751 34667 95.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.809→26.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 42 238 3071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072883
X-RAY DIFFRACTIONf_angle_d1.183911
X-RAY DIFFRACTIONf_dihedral_angle_d14.9011040
X-RAY DIFFRACTIONf_chiral_restr0.081458
X-RAY DIFFRACTIONf_plane_restr0.004497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8095-1.86270.27881310.22332769X-RAY DIFFRACTION98
1.8627-1.92280.24641390.19992752X-RAY DIFFRACTION98
1.9228-1.99150.25381460.17892745X-RAY DIFFRACTION98
1.9915-2.07120.21841560.17222755X-RAY DIFFRACTION98
2.0712-2.16540.20651320.1672753X-RAY DIFFRACTION97
2.1654-2.27950.21551490.1622744X-RAY DIFFRACTION97
2.2795-2.42230.22891480.17492744X-RAY DIFFRACTION96
2.4223-2.60920.23151510.18252743X-RAY DIFFRACTION96
2.6092-2.87150.25841420.18352741X-RAY DIFFRACTION96
2.8715-3.28630.21881640.1782723X-RAY DIFFRACTION95
3.2863-4.1380.19241370.16052721X-RAY DIFFRACTION93
4.138-26.86430.19831350.16922747X-RAY DIFFRACTION89
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)
10.4940.0494-0.44331.0355-0.16292.1413-0.02940.1448-0.0248-0.1434-0.0370.10770.076-0.30760.0480.1844-0.0138-0.02180.2473-0.01290.218311.290420.346636.0988
20.206-0.07090.22261.37481.13652.84530.030.1181-0.1092-0.1190.0788-0.14840.13840.2948-0.09430.2698-0.02140.05280.24640.00610.256128.401120.775918.54
31.0639-0.51380.22831.316-0.17641.8771-0.00570.06270.0351-0.09060.023-0.1593-0.05320.2631-0.01730.1948-0.02970.02440.2121-0.00790.237431.276724.593339.8573
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 207 )
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 365 )

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