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- PDB-3c8o: The Crystal Structure of RraA from PAO1 -

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Basic information

Entry
Database: PDB / ID: 3c8o
TitleThe Crystal Structure of RraA from PAO1
ComponentsRegulator of ribonuclease activity A
KeywordsHYDROLASE REGULATOR / RraA / PAO1 / RNase E regulater
Function / homology
Function and homology information


4-hydroxy-4-methyl-2-oxoglutarate aldolase / 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase / ribonuclease inhibitor activity / oxaloacetate decarboxylase activity / regulation of RNA metabolic process / metal ion binding
Similarity search - Function
Regulator of ribonuclease activity A / Ribonuclease E inhibitor RraA/RraA-like / Ribonuclease E inhibitor RraA/RraA-like protein / Ribonuclease E inhibitor RraA/RraA-like superfamily / Aldolase/RraA / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLuo, M. / Niu, S. / Yin, Y. / Huang, A. / Wang, D.
CitationJournal: To be published
Title: The Crystal Structure of RraA from PAO1
Authors: Luo, M. / Niu, S. / Yin, Y. / Huang, A. / Wang, D.
History
DepositionFeb 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 4, 2019Group: Advisory / Data collection
Category: diffrn_radiation / pdbx_unobs_or_zero_occ_atoms / reflns_shell
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ..._diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_radiation.pdbx_scattering_type / _reflns_shell.pdbx_Rsym_value
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Regulator of ribonuclease activity A
B: Regulator of ribonuclease activity A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,35159
Polymers34,8442
Non-polymers4,50757
Water2,612145
1
A: Regulator of ribonuclease activity A
B: Regulator of ribonuclease activity A
hetero molecules

A: Regulator of ribonuclease activity A
B: Regulator of ribonuclease activity A
hetero molecules

A: Regulator of ribonuclease activity A
B: Regulator of ribonuclease activity A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,052177
Polymers104,5316
Non-polymers13,521171
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
2
A: Regulator of ribonuclease activity A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,61830
Polymers17,4221
Non-polymers2,19629
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Regulator of ribonuclease activity A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,73229
Polymers17,4221
Non-polymers2,31128
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.679, 98.679, 180.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Regulator of ribonuclease activity A


Mass: 17421.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: K-12 / Gene: rraA / Plasmid: RraA-PW28 / Production host: Escherichia coli (E. coli) / Strain (production host): PW28 / References: UniProt: Q9I2W7

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Non-polymers , 5 types, 202 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.64 Å3/Da / Density % sol: 66.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris-HCl pH 8.5, 30% (v/v) PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 13, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 39611 / Num. obs: 39040 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 8 % / Biso Wilson estimate: 35.735 Å2 / Rmerge(I) obs: 0.0653 / Rsym value: 0.0632 / Net I/σ(I): 11.2
Reflection shellHighest resolution: 1.9 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 8 / Num. unique all: 39040 / Rsym value: 0.45 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
AUTOMARdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q5X

1q5x


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.621 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24898 2007 5.1 %RANDOM
Rwork0.22081 ---
obs0.22222 37561 95.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.542 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 294 145 2855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222668
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9862.0223477
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4435319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.47824.902102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12915390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6291512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021846
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1680.21270
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21678
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.090.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.295
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.221.51621
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.39622528
X-RAY DIFFRACTIONr_scbond_it0.64431143
X-RAY DIFFRACTIONr_scangle_it1.0824.5949
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 98 -
Rwork0.298 1820 -
obs--64.51 %
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)
11.43990.00360.01961.0644-0.13950.81290.0115-0.12660.13190.1138-0.02760.0254-0.17850.00360.0161-0.0397-0.0063-0.0111-0.0953-0.0349-0.05790.341218.649914.2765
21.1887-0.0267-0.06131.4803-0.09340.9396-0.02760.11710.0354-0.15380.00630.1082-0.0058-0.10330.0213-0.0816-0.011-0.0359-0.0391-0.0231-0.077230.681128.329730.708
30.19130.05550.1820.01960.05140.17380.028-0.00420.05120.0065-0.02290.03060.0113-0.0147-0.00520.1810.0041-0.00020.1759-0.00780.163616.613722.593421.718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1612 - 161
2X-RAY DIFFRACTION2BB1 - 1611 - 161
3X-RAY DIFFRACTION3AC - CB163 - 1911
4X-RAY DIFFRACTION3BY - GB163 - 1901

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