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- PDB-3u7j: Crystal structure of Ribose-5-phosphate isomerase A from Burkhold... -

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Basic information

Entry
Database: PDB / ID: 3u7j
TitleCrystal structure of Ribose-5-phosphate isomerase A from Burkholderia thailandensis
ComponentsRibose-5-phosphate isomerase A
KeywordsISOMERASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


D-ribose metabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / cytosol
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
: / Ribose-5-phosphate isomerase A
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionOct 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / 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.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_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: Ribose-5-phosphate isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6769
Polymers25,1351
Non-polymers5428
Water3,603200
1
A: Ribose-5-phosphate isomerase A
hetero molecules

A: Ribose-5-phosphate isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,35318
Polymers50,2692
Non-polymers1,08316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5860 Å2
ΔGint-48 kcal/mol
Surface area18440 Å2
MethodPISA
2
A: Ribose-5-phosphate isomerase A
hetero molecules

A: Ribose-5-phosphate isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,35318
Polymers50,2692
Non-polymers1,08316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area4800 Å2
ΔGint-51 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.090, 73.470, 52.010
Angle α, β, γ (deg.)90.000, 128.050, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-254-

HOH

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Components

#1: Protein Ribose-5-phosphate isomerase A / Phosphoriboisomerase A


Mass: 25134.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: rpiA, BTH_I2516 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2SVL4, ribose-5-phosphate isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Internal tracking number 225985D11. WIZARD 3/4 screen condition D11: 30%(w/v) PEG 5000 MME, 0.1M MES 6.5, 0.2M Ammonium sulfate. ButhA.00944.a.A1 PW33411 at 33.6 mg/ml. , VAPOR DIFFUSION, ...Details: Internal tracking number 225985D11. WIZARD 3/4 screen condition D11: 30%(w/v) PEG 5000 MME, 0.1M MES 6.5, 0.2M Ammonium sulfate. ButhA.00944.a.A1 PW33411 at 33.6 mg/ml. , VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 15098 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 19.877 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 21.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.153.30.09212.9265581478.9
2.15-2.210.08515351896794.3
2.21-2.280.07715.9334689694.1
2.28-2.350.0716.6339390895
2.35-2.430.07116.4335189496.2
2.43-2.510.06816.9320485594.7
2.51-2.60.0618310282795.1
2.6-2.710.05518.7298879897.3
2.71-2.830.05418.7284575996.2
2.83-2.970.0519.2278774096.5
2.97-3.130.04421.3269271297
3.13-3.320.03724.2254667797
3.32-3.550.03428.4234162297.8
3.55-3.830.03532.2223259797.5
3.83-4.20.03332.4205155097
4.2-4.70.03734.8177648696.4
4.7-5.420.04130.4161443898.2
5.42-6.640.04327.4137337696.7
6.64-9.390.03732.2104028896.3
9.39-500.03437.555216091.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.39 Å
Translation2.5 Å27.39 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1KS2

1ks2


Resolution: 2.1→47.86 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.099 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 804 5.1 %RANDOM
Rwork0.16 ---
obs0.162 15098 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å2-0.12 Å2
2--0.28 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 31 200 1923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191767
X-RAY DIFFRACTIONr_bond_other_d0.0010.021191
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9872394
X-RAY DIFFRACTIONr_angle_other_deg0.88832901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44923.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53715289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4361517
X-RAY DIFFRACTIONr_chiral_restr0.080.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021988
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02349
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 58 -
Rwork0.171 988 -
all-1046 -
obs--90.72 %
Refinement TLS params.Method: refined / Origin x: 24.252 Å / Origin y: 58.871 Å / Origin z: 37.678 Å
111213212223313233
T0.0221 Å20.0054 Å20.0192 Å2-0.015 Å20.0015 Å2--0.0259 Å2
L0.8061 °20.0383 °20.1897 °2-0.3745 °2-0.0627 °2--0.6734 °2
S0.0158 Å °-0.0109 Å °0.0307 Å °0.032 Å °-0.0138 Å °-0.014 Å °-0.0343 Å °-0.0067 Å °-0.0021 Å °

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