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

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Basic information

Entry
Database: PDB / ID: 4mam
TitleThe crystal structure of phosphoribosylaminoimidazole carboxylase ATPase subunit of Francisella tularensis subsp. tularensis SCHU S4 in complex with an ADP analog, AMP-CP
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / N5-carboxyaminoimidazole ribonucleotide synthase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.474 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 ADP analog, AMP-CP
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Sep 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 1.3Dec 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
B: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1707
Polymers83,0432
Non-polymers1,1275
Water16,628923
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-16 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.241, 85.393, 127.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. It is predicted that chains A and B form a dimer.

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Components

#1: Protein Phosphoribosylaminoimidazole carboxylase, ATPase subunit /


Mass: 41521.566 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-A12 / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-DIPHOSPHATE


Mass: 425.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N5O9P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 923 / 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: 48.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Sodium Acetate, 0.1M HEPES, 22% (w/v) PEG 4000, 15mM AM-CP, pH 7.5, 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: 1.474→25.5 Å / Num. all: 133621 / Num. obs: 133621 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 5.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 39.8
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.6 / Num. unique all: 6528 / % possible all: 98

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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: 1.474→25.493 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 6712 5.03 %Random
Rwork0.1597 ---
all0.1606 133483 --
obs0.1606 133483 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.474→25.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5681 0 72 923 6676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065976
X-RAY DIFFRACTIONf_angle_d1.158119
X-RAY DIFFRACTIONf_dihedral_angle_d13.0072184
X-RAY DIFFRACTIONf_chiral_restr0.076942
X-RAY DIFFRACTIONf_plane_restr0.0041036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4743-1.49110.26341760.23533599X-RAY DIFFRACTION85
1.4911-1.50860.22392230.21284172X-RAY DIFFRACTION100
1.5086-1.5270.23122220.20814273X-RAY DIFFRACTION100
1.527-1.54630.21052150.19324195X-RAY DIFFRACTION100
1.5463-1.56670.20452270.18944182X-RAY DIFFRACTION100
1.5667-1.58810.19132240.1854250X-RAY DIFFRACTION100
1.5881-1.61080.19982140.17634201X-RAY DIFFRACTION100
1.6108-1.63480.19492220.16644214X-RAY DIFFRACTION100
1.6348-1.66040.18552240.16464196X-RAY DIFFRACTION100
1.6604-1.68760.1962400.15714211X-RAY DIFFRACTION100
1.6876-1.71670.18182360.16444236X-RAY DIFFRACTION100
1.7167-1.74790.19992270.16254238X-RAY DIFFRACTION100
1.7479-1.78150.20052120.15924209X-RAY DIFFRACTION100
1.7815-1.81790.20192500.16124188X-RAY DIFFRACTION100
1.8179-1.85740.19862100.1574261X-RAY DIFFRACTION100
1.8574-1.90060.17112010.15764252X-RAY DIFFRACTION100
1.9006-1.94810.19482320.15774224X-RAY DIFFRACTION100
1.9481-2.00070.18132350.15574214X-RAY DIFFRACTION100
2.0007-2.05960.19782140.15534254X-RAY DIFFRACTION100
2.0596-2.1260.16322190.15064277X-RAY DIFFRACTION100
2.126-2.2020.17972010.15154281X-RAY DIFFRACTION100
2.202-2.29010.17242130.1514269X-RAY DIFFRACTION100
2.2901-2.39420.1622340.15974264X-RAY DIFFRACTION100
2.3942-2.52040.17982410.16114248X-RAY DIFFRACTION100
2.5204-2.67810.17262360.16684273X-RAY DIFFRACTION100
2.6781-2.88460.1752280.1644291X-RAY DIFFRACTION100
2.8846-3.17440.1852230.16174311X-RAY DIFFRACTION100
3.1744-3.63270.17862260.15074325X-RAY DIFFRACTION100
3.6327-4.57250.14332220.13884347X-RAY DIFFRACTION99
4.5725-25.49710.16622650.16744316X-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)
11.1660.18460.26260.6280.05071.18440.01090.1235-0.0423-0.0238-0.0212-0.1761-0.01960.17340.00970.099-0.00680.0180.14150.00790.1801-17.88261.8009-2.0445
21.3417-1.20980.60121.5492-0.3640.7449-0.1293-0.1157-0.04650.16450.1246-0.05590.02270.00780.00520.1430.0036-0.00280.14090.00640.1368-18.5749-12.786223.5685
30.8694-0.07060.27141.1148-0.92031.3433-0.0267-0.11110.04020.1739-0.0358-0.0634-0.13780.00450.06230.10330.0062-0.00740.1045-0.01440.1132-31.69562.862314.0116
41.60890.1544-0.24981.9131-0.07641.93810.0156-0.1155-0.07350.05310.0109-0.13710.20030.0731-0.01970.0797-0.003-0.00890.08510.0020.0803-40.8602-12.92914.7129
51.0809-0.15890.48860.65370.06411.0848-0.01060.1547-0.035-0.18360.0238-0.0226-0.01410.0866-0.01650.1351-0.0170.01640.1159-0.00260.086-41.8311-2.3952-25.8817
60.6503-0.1541-0.0910.1650.2662.50780.05840.14330.1184-0.2169-0.00030.0385-0.77-0.1795-0.07930.35430.0459-0.02390.16580.02240.1517-58.074116.3598-31.8529
70.7326-0.42010.43251.4721-0.27691.47210.0072-0.01920.0436-0.11230.02520.2146-0.1103-0.1779-0.02540.09070.0019-0.00550.13110.01660.1266-55.42526.454-15.0927
81.93020.05820.09632.51510.12471.504-0.09980.10340.1631-0.1690.0068-0.1079-0.1098-0.0240.08230.11250.0043-0.02250.09930.00960.1294-40.83118.9973-7.5351
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 190 )
3X-RAY DIFFRACTION3chain 'A' and (resid 191 through 297 )
4X-RAY DIFFRACTION4chain 'A' and (resid 298 through 373 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 108 )
6X-RAY DIFFRACTION6chain 'B' and (resid 109 through 202 )
7X-RAY DIFFRACTION7chain 'B' and (resid 203 through 297 )
8X-RAY DIFFRACTION8chain 'B' and (resid 298 through 365 )

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