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- PDB-3inp: 2.05 Angstrom Resolution Crystal Structure of D-ribulose-phosphat... -

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Basic information

Entry
Database: PDB / ID: 3inp
Title2.05 Angstrom Resolution Crystal Structure of D-ribulose-phosphate 3-epimerase from Francisella tularensis.
ComponentsD-ribulose-phosphate 3-epimerase
KeywordsISOMERASE / D-ribulose-phosphate 3-epimerase / idp02542 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


ribulose-phosphate 3-epimerase / D-ribulose-phosphate 3-epimerase activity / pentose catabolic process / pentose-phosphate shunt, non-oxidative branch / metal ion binding / cytosol
Similarity search - Function
Ribulose-phosphate 3-epimerase / Ribulose-phosphate 3-epimerase family signature 1. / Ribulose-phosphate 3-epimerase-like / Ribulose-phosphate 3 epimerase family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Ribulose-phosphate 3-epimerase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Scott, P. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.05 Angstrom Resolution Crystal Structure of D-ribulose-phosphate 3-epimerase from Francisella tularensis.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Scott, P. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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_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

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Assembly

Deposited unit
A: D-ribulose-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0775
Polymers26,8141
Non-polymers2634
Water2,972165
1
A: D-ribulose-phosphate 3-epimerase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)324,92060
Polymers321,76412
Non-polymers3,15648
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation26_665-x+1,-y+1,z1
crystal symmetry operation31_665-z+1,-x+1,y1
crystal symmetry operation36_665-y+1,-z+1,x1
crystal symmetry operation52_566x,-y+1,-z+11
crystal symmetry operation54_566z,-x+1,-y+11
crystal symmetry operation59_566y,-z+1,-x+11
crystal symmetry operation75_656-x+1,y,-z+11
crystal symmetry operation80_656-z+1,x,-y+11
crystal symmetry operation82_656-y+1,z,-x+11
Buried area30840 Å2
ΔGint-630 kcal/mol
Surface area94530 Å2
MethodPISA
2
A: D-ribulose-phosphate 3-epimerase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)162,46030
Polymers160,8826
Non-polymers1,57824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_455y-1/4,x+1/4,-z+3/41
crystal symmetry operation36_665-y+1,-z+1,x1
crystal symmetry operation42_554-x+3/4,z+1/4,y-1/41
crystal symmetry operation54_566z,-x+1,-y+11
crystal symmetry operation72_565-z+3/4,-y+5/4,-x+3/41
Buried area17580 Å2
ΔGint-410 kcal/mol
Surface area45100 Å2
MethodPISA
3
A: D-ribulose-phosphate 3-epimerase
hetero molecules

A: D-ribulose-phosphate 3-epimerase
hetero molecules

A: D-ribulose-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,23015
Polymers80,4413
Non-polymers78912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation36_665-y+1,-z+1,x1
crystal symmetry operation54_566z,-x+1,-y+11
Buried area5320 Å2
ΔGint-152 kcal/mol
Surface area26020 Å2
MethodPISA
4
A: D-ribulose-phosphate 3-epimerase
hetero molecules

A: D-ribulose-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,15310
Polymers53,6272
Non-polymers5268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation72_565-z+3/4,-y+5/4,-x+3/41
Buried area3530 Å2
ΔGint-120 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.080, 224.080, 224.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-225-

SO4

21A-259-

HOH

31A-368-

HOH

41A-391-

HOH

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Components

#1: Protein D-ribulose-phosphate 3-epimerase


Mass: 26813.625 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: FTT0789, FTT_0789, rpe / Plasmid: pMSCG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q5NGP6, ribulose-phosphate 3-epimerase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 4.37 Å3/Da / Density % sol: 71.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: protein solution: 7.5 mg/mL, 0.5M Sodium chloride, TRIS-HCl pH 8.3; Screen solution: JCSG+, condition B1, 0.8M Ammonium sulfate, 0.1M Citric acid pH 4.0; Cryo solution: 1.8M Ammonium ...Details: protein solution: 7.5 mg/mL, 0.5M Sodium chloride, TRIS-HCl pH 8.3; Screen solution: JCSG+, condition B1, 0.8M Ammonium sulfate, 0.1M Citric acid pH 4.0; Cryo solution: 1.8M Ammonium sulfate, 25% (w/v) Sucrose., 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: Aug 5, 2009 / Details: Diamond
RadiationMonochromator: Beryllium lenses / 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: 30690 / Num. obs: 30690 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 28.2
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 6.3 / Num. unique all: 1518 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TQJ

1tqj


Resolution: 2.05→29.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.138 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Individual Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17703 1548 5 %RANDOM
Rwork0.15833 ---
all0.15925 29116 --
obs0.15925 29116 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.424 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 12 165 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221772
X-RAY DIFFRACTIONr_bond_other_d0.0010.021156
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9642410
X-RAY DIFFRACTIONr_angle_other_deg0.86632851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1215228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.98125.19577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.93215303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.55157
X-RAY DIFFRACTIONr_chiral_restr0.0920.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211993
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_mcbond_it1.0041.51124
X-RAY DIFFRACTIONr_mcbond_other0.3391.5453
X-RAY DIFFRACTIONr_mcangle_it1.77321819
X-RAY DIFFRACTIONr_scbond_it3.2653648
X-RAY DIFFRACTIONr_scangle_it5.0584.5591
LS refinement shellResolution: 2.05→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 111 -
Rwork0.161 2110 -
obs-2110 100 %
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)
11.6701-0.40310.111.3003-0.27731.4195-0.0177-0.3517-0.07180.33170.10390.199-0.0276-0.2422-0.08610.16990.05430.0470.18370.07250.089869.5471136.4012110.1739
23.20740.3040.04251.6241-0.17052.61170.0182-0.030.11050.12630.0119-0.0029-0.13720.0383-0.03010.12340.0348-0.02690.07140.04250.060684.1556140.9527102.4561
31.30420.23830.26335.77341.62582.93580.0268-0.31710.00950.3034-0.087-0.02360.00240.15260.06030.13150.0159-0.04410.16260.04910.074388.2995136.2324107.0128
43.2370.10810.0272.38780.18322.1105-0.0042-0.1684-0.19120.0984-0.04280.05580.12880.06460.0470.1720.0646-0.01920.15130.1030.107385.6574125.6815106.1043
55.45651.4253-0.85214.1511-0.93182.06870.0158-0.4541-0.32330.4553-0.002-0.19950.1170.2172-0.01390.25170.0745-0.03890.21090.1190.108185.8096122.686114.3842
68.514-2.2747-1.92882.2188-0.32133.4383-0.4042-0.7759-0.71420.33890.3550.4330.3895-0.27570.04920.32180.0480.07780.27310.21090.222970.0347121.9855118.7359
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 66
2X-RAY DIFFRACTION2A67 - 103
3X-RAY DIFFRACTION3A104 - 125
4X-RAY DIFFRACTION4A126 - 158
5X-RAY DIFFRACTION5A159 - 192
6X-RAY DIFFRACTION6A193 - 222

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