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- PDB-2b34: Structure of MAR1 Ribonuclease from Caenorhabditis elegans -

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Basic information

Entry
Database: PDB / ID: 2b34
TitleStructure of MAR1 Ribonuclease from Caenorhabditis elegans
ComponentsMAR1 Ribonuclease
KeywordsHYDROLASE / Isochorismatase Family / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


: / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isochorismatase domain-containing protein 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.141 Å
AuthorsSchormann, N. / Karpova, E. / Li, S. / Symersky, J. / Zhang, Y. / Lu, S. / Zhou, Q. / Lin, G. / Cao, Z. / Luo, M. ...Schormann, N. / Karpova, E. / Li, S. / Symersky, J. / Zhang, Y. / Lu, S. / Zhou, Q. / Lin, G. / Cao, Z. / Luo, M. / Qiu, S. / Luan, C.-H. / Luo, D. / Huang, W. / Shang, Q. / McKinstry, A. / An, J. / Tsao, J. / Carson, M. / Stinnett, M. / Chen, Y. / Johnson, D. / Gary, R. / Arabshahi, A. / Bunzel, R. / Bray, T. / DeLucas, L. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Structure of MAR1 Ribonuclease from Caenorhabditis elegans
Authors: Schormann, N. / Karpova, E. / Li, S. / Symersky, J. / Zhang, Y. / Lu, S. / Zhou, Q. / Lin, G. / Cao, Z. / Luo, M. / Qiu, S. / Luan, C.-H. / Luo, D. / Huang, W. / Shang, Q. / McKinstry, A. / ...Authors: Schormann, N. / Karpova, E. / Li, S. / Symersky, J. / Zhang, Y. / Lu, S. / Zhou, Q. / Lin, G. / Cao, Z. / Luo, M. / Qiu, S. / Luan, C.-H. / Luo, D. / Huang, W. / Shang, Q. / McKinstry, A. / An, J. / Tsao, J. / Carson, M. / Stinnett, M. / Chen, Y. / Johnson, D. / Gary, R. / Arabshahi, A. / Bunzel, R. / Bray, T. / DeLucas, L.
History
DepositionSep 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAR1 Ribonuclease
B: MAR1 Ribonuclease
C: MAR1 Ribonuclease
D: MAR1 Ribonuclease
E: MAR1 Ribonuclease
F: MAR1 Ribonuclease
G: MAR1 Ribonuclease
H: MAR1 Ribonuclease


Theoretical massNumber of molelcules
Total (without water)175,0198
Polymers175,0198
Non-polymers00
Water10,935607
1
A: MAR1 Ribonuclease
B: MAR1 Ribonuclease
C: MAR1 Ribonuclease
D: MAR1 Ribonuclease


Theoretical massNumber of molelcules
Total (without water)87,5104
Polymers87,5104
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-29 kcal/mol
Surface area28020 Å2
MethodPISA
2
E: MAR1 Ribonuclease
F: MAR1 Ribonuclease
G: MAR1 Ribonuclease
H: MAR1 Ribonuclease


Theoretical massNumber of molelcules
Total (without water)87,5104
Polymers87,5104
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10470 Å2
ΔGint-30 kcal/mol
Surface area28360 Å2
MethodPISA
3
A: MAR1 Ribonuclease
B: MAR1 Ribonuclease
C: MAR1 Ribonuclease
D: MAR1 Ribonuclease

E: MAR1 Ribonuclease
F: MAR1 Ribonuclease
G: MAR1 Ribonuclease
H: MAR1 Ribonuclease


Theoretical massNumber of molelcules
Total (without water)175,0198
Polymers175,0198
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area23650 Å2
ΔGint-79 kcal/mol
Surface area53920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.545, 113.973, 151.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains two tetramers in an octameric assembly, with the second tetramer off-center of the first. The biological unit is probably the tetramer.

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Components

#1: Protein
MAR1 Ribonuclease / F35G2.2 / Hypothetical protein F35G2.2


Mass: 21877.426 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: Bristol N2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI / References: UniProt: Q20062
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 0.2M sodium acetate, 0.1M Tris , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 2005 / 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: 2.14→50 Å / Num. all: 84631 / Num. obs: 84631 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.4
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.168 / Num. unique all: 8022 / % possible all: 94.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The starting model was created by the Swiss-Model Server based on PDB entry 1X9G using the C. elegans target sequence (F35G2.2)

1x9g


Resolution: 2.141→41.67 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.896 / SU B: 5.843 / SU ML: 0.157 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 4183 5.1 %RANDOM
Rwork0.2195 ---
all0.2217 78165 --
obs0.2217 78165 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.126 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.89 Å20 Å2
3---1.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2.141→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11856 0 0 607 12463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02212073
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.98116418
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.18251528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.47124.561456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68152152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1171556
X-RAY DIFFRACTIONr_chiral_restr0.0720.22024
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028760
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.26098
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.28371
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2763
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3991.57906
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.679212600
X-RAY DIFFRACTIONr_scbond_it0.79534526
X-RAY DIFFRACTIONr_scangle_it1.2634.53818
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.141→2.196 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 318 -
Rwork0.225 5430 -
obs-5748 95.2 %

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