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- PDB-2otm: Crystal structure of a putative endoribonuclease (so_1960) from s... -

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Basic information

Entry
Database: PDB / ID: 2otm
TitleCrystal structure of a putative endoribonuclease (so_1960) from shewanella oneidensis mr-1 at 1.85 A resolution
ComponentsHypothetical protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyYjgF/chorismate_mutase-like, putative endoribonuclease / Endoribonuclease L-PSP/chorismate mutase-like / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / ACETATE ION / Endoribonuclease L-PSP/chorismate mutase-like domain-containing protein
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_717567.1) from Shewanella oneidensis at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE, FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,63014
Polymers51,0743
Non-polymers55511
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-42 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.083, 62.908, 78.689
Angle α, β, γ (deg.)90.000, 93.240, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-170-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEPRO6AA2 - 53 - 6
21MSEPRO6BB1 - 52 - 6
31ASNPRO6CC3 - 54 - 6
42GLUGLU2AA6 - 1527 - 153
52GLUGLU2BB6 - 1527 - 153
62GLUGLU2CC6 - 1527 - 153
73LEULEU5AA153154
83LEULEU5BB153154
93LEULEU5CC153154

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Hypothetical protein


Mass: 17024.787 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: NP_717567.1, SO_1960 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8EFL1

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Non-polymers , 5 types, 437 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 0.16M Ca(OAc)2, 20.0% Glycerol, 14.4% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97931, 0.97885
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 31, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979311
30.978851
ReflectionResolution: 1.85→29.21 Å / Num. obs: 46806 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.11 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.93.80.6671.11314834630.667100
1.9-1.953.80.5221.41264233380.52299.8
1.95-2.013.80.4231.81236132590.423100
2.01-2.073.80.3412.21206831770.341100
2.07-2.143.80.2742.71172530860.274100
2.14-2.213.80.24631127129600.246100
2.21-2.293.80.2193.41094628800.219100
2.29-2.393.80.1953.81049827570.195100
2.39-2.493.80.1624.61008626480.162100
2.49-2.623.80.1455.2974325560.145100
2.62-2.763.80.1196912723910.119100
2.76-2.933.80.0987.4883423160.098100
2.93-3.133.80.0858814721350.085100
3.13-3.383.80.0699.6770420200.069100
3.38-3.73.80.05910.7706318570.059100
3.7-4.143.80.05211.4637316740.052100
4.14-4.783.80.04912.2562114820.049100
4.78-5.853.80.05210.8482412780.052100
5.85-8.273.70.05311.536519810.053100
8.27-29.213.60.05210.819585480.05297.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→29.21 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.772 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.1
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. CALCIUM, SODIUM, GLYCEROL AND ACETATE IONS ARE MODELED BASED ON THE CRYSTALLIZATION CONDITIONS AND ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.177 2366 5.1 %RANDOM
Rwork0.151 ---
all0.152 ---
obs0.152 46806 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.687 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0.17 Å2
2--1.02 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 34 426 3908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223607
X-RAY DIFFRACTIONr_bond_other_d0.0020.022383
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9914909
X-RAY DIFFRACTIONr_angle_other_deg0.9635849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2595475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97724.178146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79515595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3821520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024068
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02697
X-RAY DIFFRACTIONr_nbd_refined0.2040.2731
X-RAY DIFFRACTIONr_nbd_other0.20.22574
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21764
X-RAY DIFFRACTIONr_nbtor_other0.0880.21981
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2332
X-RAY DIFFRACTIONr_metal_ion_refined0.170.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.7370.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3430.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.213
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2510.26
X-RAY DIFFRACTIONr_mcbond_it1.39432313
X-RAY DIFFRACTIONr_mcbond_other0.3583938
X-RAY DIFFRACTIONr_mcangle_it2.4953680
X-RAY DIFFRACTIONr_scbond_it4.46281329
X-RAY DIFFRACTIONr_scangle_it6.541111218
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A847TIGHT POSITIONAL0.080.05
2B847TIGHT POSITIONAL0.040.05
3C847TIGHT POSITIONAL0.070.05
1A924MEDIUM POSITIONAL0.390.5
2B924MEDIUM POSITIONAL0.340.5
3C924MEDIUM POSITIONAL0.340.5
1A43LOOSE POSITIONAL0.685
2B43LOOSE POSITIONAL0.575
3C43LOOSE POSITIONAL0.685
1A847TIGHT THERMAL0.190.5
2B847TIGHT THERMAL0.180.5
3C847TIGHT THERMAL0.190.5
1A924MEDIUM THERMAL0.862
2B924MEDIUM THERMAL0.92
3C924MEDIUM THERMAL0.92
1A43LOOSE THERMAL1.6110
2B43LOOSE THERMAL4.5910
3C43LOOSE THERMAL5.7510
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 160 -
Rwork0.226 3301 -
obs-3461 99.97 %
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)
10.34920.1350.17670.43040.29020.9696-0.00170.0007-0.0179-0.0484-0.0193-0.02890.0443-0.07650.0209-0.0189-0.0020.0034-0.0257-0.015-0.038521.914422.825919.4045
20.2864-0.04870.21490.5767-0.24840.6624-0.01530.0452-0.0119-0.0261-0.0192-0.0186-0.07330.03540.0345-0.0099-0.001-0.006-0.02590.0063-0.04336.869443.539619.2701
30.79930.30520.27680.7536-0.23911.0230.02980.1454-0.1584-0.0844-0.0337-0.20410.13410.1850.004-0.02090.05230.02280.0116-0.02260.052346.8720.292919.7437
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 1533 - 154
22BB1 - 1532 - 154
33CC3 - 1534 - 154

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