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- PDB-4nml: 2.60 Angstrom resolution crystal structure of putative ribose 5-p... -

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Basic information

Entry
Database: PDB / ID: 4nml
Title2.60 Angstrom resolution crystal structure of putative ribose 5-phosphate isomerase from Toxoplasma gondii ME49 in complex with DL-Malic acid
ComponentsRibulose 5-phosphate isomerase
KeywordsISOMERASE / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch
Similarity search - Function
Ribose-5-phosphate isomerase, type A, subgroup / Ribose 5-phosphate isomerase, type A / Ribose 5-phosphate isomerase A (phosphoriboisomerase A) / Rossmann fold - #1360 / ACT domain / NagB/RpiA transferase-like / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MALATE / Ribose-5-phosphate isomerase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsHalavaty, A.S. / Dubrovska, I. / Flores, K. / Shanmugam, D. / Shuvalova, L. / Roos, D. / Ruan, J. / Ngo, H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Front Cell Infect Microbiol / Year: 2018
Title: CSGID Solves Structures and Identifies Phenotypes for Five Enzymes in Toxoplasma gondii .
Authors: Lykins, J.D. / Filippova, E.V. / Halavaty, A.S. / Minasov, G. / Zhou, Y. / Dubrovska, I. / Flores, K.J. / Shuvalova, L.A. / Ruan, J. / El Bissati, K. / Dovgin, S. / Roberts, C.W. / Woods, S. ...Authors: Lykins, J.D. / Filippova, E.V. / Halavaty, A.S. / Minasov, G. / Zhou, Y. / Dubrovska, I. / Flores, K.J. / Shuvalova, L.A. / Ruan, J. / El Bissati, K. / Dovgin, S. / Roberts, C.W. / Woods, S. / Moulton, J.D. / Moulton, H. / McPhillie, M.J. / Muench, S.P. / Fishwick, C.W.G. / Sabini, E. / Shanmugam, D. / Roos, D.S. / McLeod, R. / Anderson, W.F. / Ngo, H.M.
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 27, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9304
Polymers29,7251
Non-polymers2053
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ribulose 5-phosphate isomerase
hetero molecules

A: Ribulose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8608
Polymers59,4502
Non-polymers4106
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Buried area3340 Å2
ΔGint-61 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.590, 95.590, 112.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21A-447-

HOH

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Components

#1: Protein Ribulose 5-phosphate isomerase


Mass: 29724.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: TGME49_239310 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: S8GQK2, ribose-5-phosphate isomerase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 4.33 Å3/Da / Density % sol: 71.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein at 7.1 mg/mL in 10 mM Tris-HCl pH 8.3 500 mM NaCl 5 mM BME, crystallization The JCSG+ suite (F8 or #68): 2.1 M DL-Malic acid pH 7.0, cryo 1:1 (v/v) 50% sucrose and F8, VAPOR ...Details: protein at 7.1 mg/mL in 10 mM Tris-HCl pH 8.3 500 mM NaCl 5 mM BME, crystallization The JCSG+ suite (F8 or #68): 2.1 M DL-Malic acid pH 7.0, cryo 1:1 (v/v) 50% sucrose and F8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2013 / Details: Be lenses
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 16774 / Num. obs: 16774 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Biso Wilson estimate: 61.4 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 44.9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 5.4 / Num. unique all: 818 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.556 / SU ML: 0.125 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20477 842 5.1 %RANDOM
Rwork0.16449 ---
obs0.16643 15802 99.84 %-
all-15802 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.853 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.9 Å2-0 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 11 71 1948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191938
X-RAY DIFFRACTIONr_bond_other_d0.0010.021909
X-RAY DIFFRACTIONr_angle_refined_deg1.7112.0012619
X-RAY DIFFRACTIONr_angle_other_deg0.8134403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3465256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52123.94776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18315326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8191515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02400
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 63 -
Rwork0.258 1134 -
obs-1134 99.83 %
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)
11.77280.67360.07431.45-0.9533.9358-0.12240.33650.0618-0.05260.1028-0.0303-0.64670.32290.01960.1656-0.1361-0.02190.4204-0.09690.152717.083858.19897.1733
21.406-0.10010.00520.9604-0.60666.8607-0.13170.1959-0.222-0.17040.13330.17320.9195-0.0096-0.00160.1506-0.0416-0.00580.2808-0.13970.181411.662240.408816.7612
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 130
2X-RAY DIFFRACTION2A131 - 257

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