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- PDB-4nu7: 2.05 Angstrom Crystal Structure of Ribulose-phosphate 3-epimerase... -

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Basic information

Entry
Database: PDB / ID: 4nu7
Title2.05 Angstrom Crystal Structure of Ribulose-phosphate 3-epimerase from Toxoplasma gondii.
ComponentsRibulose-phosphate 3-epimerasePhosphopentose epimerase
KeywordsISOMERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / TIM Barrel / ribulose-phosphate 3-epimerase
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / :
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMinasov, G. / Ruan, J. / Ngo, H. / Shuvalova, L. / Dubrovska, I. / Flores, K. / 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
DepositionDec 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 27, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose-phosphate 3-epimerase
B: Ribulose-phosphate 3-epimerase
C: Ribulose-phosphate 3-epimerase
D: Ribulose-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,46925
Polymers105,8774
Non-polymers1,59221
Water9,242513
1
A: Ribulose-phosphate 3-epimerase
C: Ribulose-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,84814
Polymers52,9392
Non-polymers91012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-162 kcal/mol
Surface area17360 Å2
MethodPISA
2
B: Ribulose-phosphate 3-epimerase
D: Ribulose-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,62111
Polymers52,9392
Non-polymers6829
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-190 kcal/mol
Surface area17450 Å2
MethodPISA
3
A: Ribulose-phosphate 3-epimerase
C: Ribulose-phosphate 3-epimerase
hetero molecules

A: Ribulose-phosphate 3-epimerase
C: Ribulose-phosphate 3-epimerase
hetero molecules

A: Ribulose-phosphate 3-epimerase
C: Ribulose-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,54542
Polymers158,8166
Non-polymers2,72936
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13410 Å2
ΔGint-547 kcal/mol
Surface area49150 Å2
MethodPISA
4
B: Ribulose-phosphate 3-epimerase
D: Ribulose-phosphate 3-epimerase
hetero molecules

B: Ribulose-phosphate 3-epimerase
D: Ribulose-phosphate 3-epimerase
hetero molecules

B: Ribulose-phosphate 3-epimerase
D: Ribulose-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,86233
Polymers158,8166
Non-polymers2,04627
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area13240 Å2
ΔGint-598 kcal/mol
Surface area49560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.510, 138.510, 349.329
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Ribulose-phosphate 3-epimerase / Phosphopentose epimerase


Mass: 26469.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: RPE, TGVEG_004130 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pMagic / References: UniProt: B9PPN9, ribulose-phosphate 3-epimerase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: Protein: 7.4 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: Classics II (A1), 2M Ammonium sulfate, 0.1M Citric acid pH 3.5. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 81012 / Num. obs: 81012 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 20.1
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3999 / Rsym value: 0.615 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.8.0046refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QC3

3qc3


Resolution: 2.05→29.88 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 6.973 / SU ML: 0.093
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18685 4056 5 %RANDOM
Rwork0.14941 ---
all0.15126 76865 --
obs0.15126 76865 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å2-0 Å2
2--0.12 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6761 0 69 513 7343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197266
X-RAY DIFFRACTIONr_bond_other_d0.0010.027003
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9719877
X-RAY DIFFRACTIONr_angle_other_deg0.719316162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1125965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95624.502291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.142151230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1991538
X-RAY DIFFRACTIONr_chiral_restr0.0870.21101
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0218394
X-RAY DIFFRACTIONr_gen_planes_other0.0170.021596
X-RAY DIFFRACTIONr_mcbond_it1.8342.1973779
X-RAY DIFFRACTIONr_mcbond_other1.8332.1963778
X-RAY DIFFRACTIONr_mcangle_it2.733.2744771
X-RAY DIFFRACTIONr_mcangle_other2.7323.2754772
X-RAY DIFFRACTIONr_scbond_it3.1642.583487
X-RAY DIFFRACTIONr_scbond_other2.9972.5373437
X-RAY DIFFRACTIONr_scangle_other4.7033.6545034
X-RAY DIFFRACTIONr_long_range_B_refined7.95619.2478611
X-RAY DIFFRACTIONr_long_range_B_other7.73718.5058375
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 311 -
Rwork0.219 5594 -
obs-5594 99.92 %
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)
15.9112-4.1803-3.40156.27771.89582.43820.1179-0.08690.20260.21140.0032-0.41630.22360.0063-0.1210.33360.015-0.05490.4132-0.12190.12476.914931.13655.2416
21.9083-0.714-0.75642.134-0.48053.1438-0.0534-0.38470.11290.09790.1826-0.21060.31020.1708-0.12920.14960.019-0.00660.1439-0.03790.03776.98927.38248.5536
31.76920.1755-0.19031.9942-0.88272.51390.0816-0.02740.0377-0.23620.0050.06190.2386-0.1252-0.08660.1411-0.0210.01580.0569-0.00580.0113-3.658730.650737.5566
42.42630.28550.01455.81180.15142.18360.1434-0.17230.1116-0.3222-0.0890.3598-0.098-0.3009-0.05440.13650.00370.00790.1347-0.02880.039-8.126737.244742.1286
52.7141-0.3552-0.292.98860.50653.58310.0974-0.39750.48170.05810.0254-0.1382-0.43980.0001-0.12280.1938-0.02750.05660.1574-0.12810.1277-0.342245.34751.1503
64.7526-2.2466-2.44595.95830.99945.7141-0.0547-0.62190.2910.36550.2568-0.5066-0.05850.5942-0.20210.234-0.0099-0.03770.4493-0.22330.14426.655839.46662.901
74.96451.7383.53141.82271.30346.76890.1125-0.1078-0.3974-0.1020.0103-0.21940.2027-0.0612-0.12280.1092-0.0447-0.030.02450.01430.068823.894662.235318.7339
82.96541.3992-0.15691.12420.02711.4621-0.0389-0.0036-0.3387-0.03580.0052-0.26750.1447-0.07770.03360.1075-0.0227-0.02650.04770.00020.081619.572655.035720.184
91.76560.4124-0.27543.39210.18272.20420.105-0.4307-0.47550.3695-0.2421-0.21490.32-0.13560.1370.1555-0.0704-0.05690.1410.10530.152620.337349.421734.0642
101.4613-0.22191.34334.0337-0.35632.95840.2075-0.372-0.11220.2257-0.1311-0.0936-0.0516-0.2561-0.07640.197-0.07-0.05740.20180.05410.024719.521263.819837.087
111.41840.70360.93892.4513-1.16033.36480.0542-0.2944-0.10380.2992-0.0628-0.1699-0.2651-0.09770.00850.1468-0.0355-0.06560.11250.03630.039625.775868.355932.28
123.64262.3714-0.14114.6616-0.08994.2270.0519-0.0681-0.10540.14190.0416-0.02930.0257-0.0137-0.09350.1331-0.0611-0.05660.03660.02890.031927.799973.126220.6938
134.9528-2.7568-2.37693.01852.09874.84070.1236-0.16370.50270.07210.0718-0.4266-0.1163-0.0433-0.19540.1620.0390.04210.0258-0.01620.116326.237914.572341.1141
142.1887-1.66320.282.6041-0.09141.77170.0979-0.05460.4927-0.1519-0.0828-0.5847-0.07020.0083-0.01510.1590.0080.10190.0261-0.0040.186821.725826.442133.6857
1510.85781.95559.03743.07032.797411.55180.19460.65941.3851-0.6873-0.554-0.7913-0.54160.48450.35940.55790.1130.34350.28730.25340.677227.63832.127220.3415
165.43952.326-0.0537.34062.95437.04140.5020.41150.0594-0.6854-0.2195-0.6139-0.1288-0.199-0.28240.31050.15630.20320.08840.09940.158323.414221.424720.4855
171.6425-0.961-0.45711.3399-0.22211.12070.21440.17620.1063-0.3224-0.1244-0.22050.143-0.0425-0.090.28080.05460.10940.0720.02640.104424.018311.403424.4952
181.905-1.3719-1.56244.9099-1.38998.69090.1884-0.070.2549-0.2411-0.1032-0.19250.13330.1906-0.08520.20590.06230.0650.0320.00620.065229.58263.652635.7466
196.61883.95063.31595.09860.93742.6212-0.05770.0973-0.238-0.11780.0248-0.2352-0.2214-0.16740.03290.156-0.00360.02510.2734-0.13940.09783.129648.30242.8757
202.17140.9129-0.09021.5706-0.82242.30610.03660.2766-0.15920.00150.0446-0.1047-0.22160.1877-0.08120.0875-0.03580.0230.0892-0.03940.02413.846752.113110.033
212.52160.0274-0.18971.722-1.12592.65230.056-0.1221-0.10760.1873-0.02010.059-0.2484-0.0278-0.03580.1117-0.00560.01330.03450.00090.0081-7.324650.012520.6102
222.92320.134-0.22665.7265-0.09922.10290.11830.182-0.26230.2794-0.08890.31210.0955-0.2351-0.02930.0954-0.02210.02320.0732-0.03730.0567-11.663243.573315.582
233.25450.2175-0.13921.6804-0.01433.6340.01770.37-0.575-0.08010.0099-0.15780.4058-0.0031-0.02760.1491-0.01830.01180.0864-0.12140.1865-4.667534.59317.0637
242.67452.65691.30073.96561.98265.6214-0.1490.5346-0.5624-0.15370.3329-0.47840.0490.2643-0.18380.1048-0.0290.04540.3133-0.22750.18733.226240.1747-4.1489
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 26
2X-RAY DIFFRACTION2A27 - 71
3X-RAY DIFFRACTION3A72 - 111
4X-RAY DIFFRACTION4A112 - 144
5X-RAY DIFFRACTION5A145 - 204
6X-RAY DIFFRACTION6A205 - 228
7X-RAY DIFFRACTION7B4 - 26
8X-RAY DIFFRACTION8B27 - 75
9X-RAY DIFFRACTION9B76 - 129
10X-RAY DIFFRACTION10B130 - 168
11X-RAY DIFFRACTION11B169 - 207
12X-RAY DIFFRACTION12B208 - 228
13X-RAY DIFFRACTION13C4 - 33
14X-RAY DIFFRACTION14C34 - 102
15X-RAY DIFFRACTION15C103 - 115
16X-RAY DIFFRACTION16C116 - 134
17X-RAY DIFFRACTION17C135 - 208
18X-RAY DIFFRACTION18C209 - 230
19X-RAY DIFFRACTION19D3 - 26
20X-RAY DIFFRACTION20D27 - 72
21X-RAY DIFFRACTION21D73 - 111
22X-RAY DIFFRACTION22D112 - 146
23X-RAY DIFFRACTION23D147 - 202
24X-RAY DIFFRACTION24D203 - 228

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