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- PDB-4x84: Crystal structure of Ribose-5-phosphate isomerase A from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 4x84
TitleCrystal structure of Ribose-5-phosphate isomerase A from Pseudomonas aeruginosa
ComponentsRibose-5-phosphate isomerase A
KeywordsISOMERASE / SSGCID / Pseudomonas aeruginosa / Ribose-5-phosphate isomerase A / Phosphoriboisomerase A / PRI / Structural Genomics / 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
CITRATE ANION / Ribose-5-phosphate isomerase A
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Ribose-5-phosphate isomerase A from Pseudomonas aeruginosa
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionDec 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribose-5-phosphate isomerase A
B: Ribose-5-phosphate isomerase A
C: Ribose-5-phosphate isomerase A
D: Ribose-5-phosphate isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8788
Polymers99,1214
Non-polymers7564
Water27,9051549
1
A: Ribose-5-phosphate isomerase A
D: Ribose-5-phosphate isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9394
Polymers49,5612
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-12 kcal/mol
Surface area17900 Å2
MethodPISA
2
B: Ribose-5-phosphate isomerase A
C: Ribose-5-phosphate isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9394
Polymers49,5612
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-11 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.070, 142.790, 161.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a tetramer, there are two biological unics in the asu: chains AD and BC

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Components

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


Mass: 24780.355 Da / Num. of mol.: 4 / Fragment: PsaeA.00944.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: rpiA, PA0330 / Plasmid: PsaeA.01152.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I6G1, ribose-5-phosphate isomerase
#2: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1549 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Moledular Dimensions, Morpheus screen G4: 20mM each Na-Formate; NH4-Acetate; Na3-Citrate; NaKTartrate (racemic); Na-Oxamate; 12.5% each MPD (racemic); PEG 1K; PEG 3350; 100mM Imidazole; MES ...Details: Moledular Dimensions, Morpheus screen G4: 20mM each Na-Formate; NH4-Acetate; Na3-Citrate; NaKTartrate (racemic); Na-Oxamate; 12.5% each MPD (racemic); PEG 1K; PEG 3350; 100mM Imidazole; MES (acid) pH 6.5; PsaeA.00944.a.B1.PS02170 at 29.9mg/ml; direct cryo; tray 258189, puck frv7-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 29, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 262311 / Num. obs: 261250 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 8.68 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.076 / Χ2: 0.95 / Net I/σ(I): 14 / Num. measured all: 1258596
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.25-1.284.80.870.4953.229169319247192310.55599.9
1.28-1.320.8840.443.628904418677186590.49499.9
1.32-1.360.9090.3864.078728818210181950.43399.9
1.36-1.40.930.3314.768526317713176930.37199.9
1.4-1.440.9490.2765.648294117175171550.30999.9
1.44-1.490.9630.2246.918053216615166020.25199.9
1.49-1.550.9770.1798.57810816074160660.2100
1.55-1.610.9840.14910.067562115486154710.16699.9
1.61-1.690.9870.12511.657260414852148300.13999.9
1.69-1.770.9910.10513.716989214243142270.11799.9
1.77-1.860.9940.08416.496663013554135380.09499.9
1.86-1.980.9960.06919.836234712807127660.07799.7
1.98-2.110.9970.05723.675857812094120210.06399.4
2.11-2.280.9970.0526.485437011301112470.05699.5
2.28-2.50.9970.04628.294949510374103020.05199.3
2.5-2.80.9980.04130.9644452945693720.04699.1
2.8-3.230.9980.03733.639040840083060.04298.9
3.23-3.950.9980.03436.932564713369940.03898.1
3.95-5.590.9980.03437.8924992562454790.03897.4
5.590.9970.03536.7113142327630960.0494.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.02 Å42.18 Å
Translation6.02 Å42.18 Å

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Processing

Software
NameClassification
XDSdata reduction
PHASERphasing
ARPmodel building
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3enq

3enq


Resolution: 1.25→45.649 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1574 2000 0.77 %Random selection
Rwork0.1383 259196 --
obs0.1385 261196 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.09 Å2 / Biso mean: 14.3851 Å2 / Biso min: 4.78 Å2
Refinement stepCycle: final / Resolution: 1.25→45.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6719 0 52 1578 8349
Biso mean--9.31 25.4 -
Num. residues----899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057151
X-RAY DIFFRACTIONf_angle_d1.1089771
X-RAY DIFFRACTIONf_chiral_restr0.0721172
X-RAY DIFFRACTIONf_plane_restr0.0051286
X-RAY DIFFRACTIONf_dihedral_angle_d12.0232696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.28130.21321420.16681839118533100
1.2813-1.31590.20641420.1591832618468100
1.3159-1.35460.17311410.15011840918550100
1.3546-1.39840.16961420.14231838118523100
1.3984-1.44830.16231420.13391841918561100
1.4483-1.50630.16341430.12471846518608100
1.5063-1.57490.16261430.11711849218635100
1.5749-1.65790.15231420.11781846618608100
1.6579-1.76180.14321430.1221850518648100
1.7618-1.89780.15651430.13081854918692100
1.8978-2.08880.1381430.13081854518688100
2.0888-2.39110.16011430.13561862318766100
2.3911-3.01240.15751440.1483186511879599
3.0124-45.67910.14931470.1468189741912197

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