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- PDB-9bki: Crystal structure of Rid family protein ACIAD3089 from Acinetobac... -

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Basic information

Entry
Database: PDB / ID: 9bki
TitleCrystal structure of Rid family protein ACIAD3089 from Acinetobacter baylyi in C2 space group
ComponentsRid family protein ACIAD3089
KeywordsHYDROLASE / Rid family protein / deamination / stress / Endoribonuclease L-PSP/chorismate mutase-like domain-containing protein
Function / homologyEndoribonuclease L-PSP/chorismate mutase-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / Uncharacterized protein
Function and homology information
Biological speciesAcinetobacter baylyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsZhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Rid family protein ACIAD3089 from Acinetobacter baylyi in C2 space group
Authors: Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
History
DepositionApr 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rid family protein ACIAD3089
B: Rid family protein ACIAD3089
C: Rid family protein ACIAD3089
D: Rid family protein ACIAD3089
E: Rid family protein ACIAD3089
F: Rid family protein ACIAD3089
G: Rid family protein ACIAD3089
H: Rid family protein ACIAD3089
I: Rid family protein ACIAD3089


Theoretical massNumber of molelcules
Total (without water)160,1029
Polymers160,1029
Non-polymers00
Water2,540141
1
A: Rid family protein ACIAD3089
B: Rid family protein ACIAD3089
C: Rid family protein ACIAD3089


Theoretical massNumber of molelcules
Total (without water)53,3673
Polymers53,3673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Rid family protein ACIAD3089
F: Rid family protein ACIAD3089

E: Rid family protein ACIAD3089


Theoretical massNumber of molelcules
Total (without water)53,3673
Polymers53,3673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
3
I: Rid family protein ACIAD3089

G: Rid family protein ACIAD3089

H: Rid family protein ACIAD3089


Theoretical massNumber of molelcules
Total (without water)53,3673
Polymers53,3673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Unit cell
Length a, b, c (Å)159.270, 77.380, 150.400
Angle α, β, γ (deg.)90.000, 97.418, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 18 or resid 29 through 158))
d_2ens_1(chain "B" and (resid 2 through 18 or resid 29 through 158))
d_3ens_1(chain "C" and (resid 2 through 18 or resid 29 through 158))
d_4ens_1(chain "D" and (resid 2 through 18 or resid 29 through 158))
d_5ens_1(chain "E" and (resid 2 through 18 or resid 29 through 158))
d_6ens_1chain "F"
d_7ens_1(chain "G" and (resid 2 through 18 or resid 29 through 158))
d_8ens_1(chain "H" and (resid 2 through 18 or resid 29 through 158))
d_9ens_1(chain "I" and (resid 2 through 18 or resid 29 through 158))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASNASNPHEPHEAA2 - 182 - 18
d_12THRTHRGLNGLNAA29 - 15829 - 158
d_21ASNASNPHEPHEBB2 - 182 - 18
d_22THRTHRGLNGLNBB29 - 15829 - 158
d_31ASNASNPHEPHECC2 - 182 - 18
d_32THRTHRGLNGLNCC29 - 15829 - 158
d_41ASNASNPHEPHEDD2 - 182 - 18
d_42THRTHRGLNGLNDD29 - 15829 - 158
d_51ASNASNPHEPHEEE2 - 182 - 18
d_52THRTHRGLNGLNEE29 - 15829 - 158
d_61ASNASNGLNGLNFF2 - 1582 - 158
d_71ASNASNPHEPHEGG2 - 182 - 18
d_72THRTHRGLNGLNGG29 - 15829 - 158
d_81ASNASNPHEPHEHH2 - 182 - 18
d_82THRTHRGLNGLNHH29 - 15829 - 158
d_91ASNASNPHEPHEII2 - 182 - 18
d_92THRTHRGLNGLNII29 - 15829 - 158

NCS oper:
IDCodeMatrixVector
1given(-0.291438745972, 0.916868196562, 0.272793268758), (-0.192297844647, 0.223197738274, -0.955617239575), (-0.937061895656, -0.330961447548, 0.111263309078)47.0110202474, 56.6335054411, 88.1763639462
2given(-0.289094785942, -0.17937650662, -0.940344763166), (0.922372296806, 0.210724214025, -0.323766353577), (0.256229488597, -0.960947123673, 0.104532648858)107.698187888, -27.2149190757, 32.6278556658
3given(-0.90007869604, -0.277530551021, -0.335909413659), (-0.344599040763, -0.0184054732061, 0.938569517756), (-0.266664287147, 0.960540489415, -0.079070387341)53.0672715944, -38.9718453296, 65.1146198478
4given(0.630395818516, -0.776259987695, -0.00464149781828), (-0.775979262339, -0.63031002691, 0.0237792850513), (-0.0213844901361, -0.0113886558105, -0.999706457967)44.314950032, -11.667496634, 99.4695310076
5given(-0.0334641586879, 0.405166354505, 0.913630327463), (0.324902795202, -0.860080390961, 0.393319074993), (0.945155185011, 0.310003139115, -0.102857814413)-50.0181036657, -43.0096449683, 9.49296905088
6given(0.321263456731, -0.694128022437, 0.644186370422), (-0.265745681443, 0.5868320427, 0.7648577557), (-0.908938405044, -0.416910592488, 0.00406616622694)-25.9844197004, -73.4668975347, 44.83343265
7given(-0.535158050616, -0.844751802273, -0.000503405774775), (0.835529892974, -0.529403512342, 0.147043255767), (-0.124481560107, 0.0782707715396, 0.989129934597)46.2244211314, -16.9967340486, -40.898101371
8given(0.612648195609, 0.0833130990312, -0.78595236239), (-0.703701631224, -0.395219516945, -0.590428274762), (-0.359814122332, 0.914800776648, -0.183502960235)69.0910456947, 53.4944677476, 23.4620570161

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Components

#1: Protein
Rid family protein ACIAD3089


Mass: 17789.084 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi (bacteria) / Gene: ACIAD3089 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6F828
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M SODIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 70631 / % possible obs: 99.4 % / Redundancy: 6.94 % / Biso Wilson estimate: 50.3 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.85
Reflection shellResolution: 2.38→2.44 Å / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 3.88 / Num. unique obs: 4701

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→43.53 Å / SU ML: 0.2943 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 26.4261
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2429 2000 2.83 %
Rwork0.2001 68631 -
obs0.2013 70631 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.17 Å2
Refinement stepCycle: LAST / Resolution: 2.38→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10305 0 0 141 10446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008310436
X-RAY DIFFRACTIONf_angle_d1.109314109
X-RAY DIFFRACTIONf_chiral_restr0.06321684
X-RAY DIFFRACTIONf_plane_restr0.00761817
X-RAY DIFFRACTIONf_dihedral_angle_d18.4953761
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.03413222643
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.838921121569
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.937285473758
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.699771817693
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.873366038404
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.873951361425
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS0.901719471021
ens_1d_9AAX-RAY DIFFRACTIONTorsion NCS0.863168660147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.440.33511330.2684568X-RAY DIFFRACTION91.21
2.44-2.510.29181370.24484676X-RAY DIFFRACTION92.5
2.51-2.580.31911380.24294757X-RAY DIFFRACTION94.13
2.58-2.660.29311400.22654787X-RAY DIFFRACTION95.19
2.66-2.760.241420.22734871X-RAY DIFFRACTION96.26
2.76-2.870.28971410.23274862X-RAY DIFFRACTION96.58
2.87-30.26021400.25164795X-RAY DIFFRACTION95.31
3-3.160.27911440.23774954X-RAY DIFFRACTION98.44
3.16-3.350.25361460.21965010X-RAY DIFFRACTION98.68
3.35-3.610.23661470.2055039X-RAY DIFFRACTION99.37
3.61-3.980.23491460.19115028X-RAY DIFFRACTION99.42
3.98-4.550.18931460.16395023X-RAY DIFFRACTION98.08
4.55-5.730.23141480.17275079X-RAY DIFFRACTION99.89
5.73-43.530.24511520.19075182X-RAY DIFFRACTION98.83

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