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- PDB-3dxo: CRYSTAL STRUCTURE OF A PUTATIVE ISOMERASE OF THE SNOAL-LIKE FAMIL... -

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Basic information

Entry
Database: PDB / ID: 3dxo
TitleCRYSTAL STRUCTURE OF A PUTATIVE ISOMERASE OF THE SNOAL-LIKE FAMILY (ATU_0744) FROM AGROBACTERIUM TUMEFACIENS STR. C58 AT 2.70 A RESOLUTION
Componentsuncharacterized SnoaL-like Protein
KeywordsISOMERASE / PUTATIVE ISOMERASE OF THE SNOAL-LIKE FAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / SnoaL-like domain-containing protein
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of SnoaL-like Protein with Unknown Function (17739112) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 9, 2020Group: Derived calculations / Refinement description / Category: refine / struct_site
Item: _refine.details / _struct_site.pdbx_auth_asym_id ..._refine.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized SnoaL-like Protein
B: uncharacterized SnoaL-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4417
Polymers26,8672
Non-polymers5755
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint4 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.570, 119.570, 94.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSEGLUGLU1AA1 - 182 - 19
21MSEMSEGLUGLU1BB1 - 182 - 19
32ASPASPASPASP2AA1920
42ASPASPASPASP2BB1920
53ASNASNARGARG1AA20 - 2421 - 25
63ASNASNARGARG1BB20 - 2421 - 25
74HISHISHISHIS2AA2526
84HISHISHISHIS2BB2526
95LEULEUARGARG1AA26 - 6527 - 66
105LEULEUARGARG1BB26 - 6527 - 66
116PHEPHEPHEPHE2AA6667
126PHEPHEPHEPHE2BB6667
137VALVALGLYGLY1AA67 - 11768 - 118
147VALVALGLYGLY1BB67 - 11768 - 118
DetailsAUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS THAT FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS.

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Components

#1: Protein uncharacterized SnoaL-like Protein


Mass: 13433.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Gene: 17739112, AGR_C_1349, Atu0744 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q7D0S4
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 5.0000% PEG-6000, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97968,0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 27, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979681
30.979461
ReflectionResolution: 2.7→28.724 Å / Num. obs: 11229 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 49.301 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 7.04
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.7-2.80.4541.94048209897.8
2.8-2.910.3632.33899200698.8
2.91-3.040.2883.13940202999.1
3.04-3.20.2134.13936204198.5
3.2-3.40.1465.73947203898.8
3.4-3.660.1047.93963203899.1
3.66-4.030.0859.54031207399
4.03-4.60.06511.83980203798.8
4.6-5.770.06411.33921197096.1
5.770.04813.24076196190.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→28.724 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.885 / SU B: 23.031 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.515 / ESU R Free: 0.307
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. PEG FRAGMENTS (PEG AND PGE) FROM THE PEG6000 AND PEG200 PRESENT IN THE CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 542 4.8 %RANDOM
Rwork0.231 ---
obs0.233 11216 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.437 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.7→28.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 38 44 1910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211922
X-RAY DIFFRACTIONr_bond_other_d0.0040.021299
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9272595
X-RAY DIFFRACTIONr_angle_other_deg1.01333125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3985238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.05824105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91115287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4571517
X-RAY DIFFRACTIONr_chiral_restr0.0890.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022198
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02413
X-RAY DIFFRACTIONr_nbd_refined0.2220.2395
X-RAY DIFFRACTIONr_nbd_other0.2060.21343
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2906
X-RAY DIFFRACTIONr_nbtor_other0.0930.21061
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2990.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.24
X-RAY DIFFRACTIONr_mcbond_it0.77221254
X-RAY DIFFRACTIONr_mcbond_other0.2272491
X-RAY DIFFRACTIONr_mcangle_it1.06131850
X-RAY DIFFRACTIONr_scbond_it0.8312837
X-RAY DIFFRACTIONr_scangle_it1.3013742
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1472TIGHT POSITIONAL0.050.05
20MEDIUM POSITIONAL0.410.5
1472TIGHT THERMAL0.090.5
20MEDIUM THERMAL0.482
LS refinement shellResolution: 2.702→2.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 37 -
Rwork0.311 784 -
all-821 -
obs--99.76 %
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)
12.036-2.4810.26684.3034-0.23124.56240.00360-0.00970.13840.0333-0.11510.16670.2396-0.0369-0.04280.03220.0073-0.16140.0017-0.11848.007887.7967-10.3886
22.3809-2.00760.18654.9032-0.1023.18550.06560.03040.1222-0.3737-0.1573-0.2761-0.3594-0.04990.0917-0.03180.1433-0.0196-0.0427-0.0281-0.157721.569266.1577-20.798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1172 - 118
2X-RAY DIFFRACTION2BB1 - 1182 - 119

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