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- PDB-3oql: Crystal structure of a TenA homolog (PSPTO1738) from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3oql
TitleCrystal structure of a TenA homolog (PSPTO1738) from Pseudomonas syringae pv. tomato str. DC3000 at 2.54 A resolution
ComponentsTenA homolog
KeywordsTRANSCRIPTION / TRANSCRIPTIONAL ACTIVATOR / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyIron-containing redox enzyme / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.54 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a TenA homolog (PSPTO1738) from Pseudomonas syringae pv. tomato str. DC3000 at 2.54 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TenA homolog
B: TenA homolog
C: TenA homolog
D: TenA homolog


Theoretical massNumber of molelcules
Total (without water)122,5804
Polymers122,5804
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-45 kcal/mol
Surface area38490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.339, 67.339, 479.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein
TenA homolog


Mass: 30645.104 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: PSPTO1738, PSPTO_1738 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q885U3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.21
Details: 0.84M sodium citrate, 0.1M Imidazole pH 8.21, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97922,0.97898
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2010 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979221
30.978981
ReflectionResolution: 2.54→29.88 Å / Num. obs: 37971 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 70.646 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.55-2.640.8221.625491648894.1
2.64-2.750.6082.329122719999.9
2.75-2.870.4683270206646100
2.87-3.020.3573.8279296877100
3.02-3.210.2395.7286607059100
3.21-3.460.1439.3282146931100
3.46-3.80.08415.1277616846100
3.8-4.350.0621.4281296985100
4.35-5.460.04924.6278116898100
5.460.03528.928082708599.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata processing
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.54→29.88 Å / Cor.coef. Fo:Fc: 0.9546 / Cor.coef. Fo:Fc free: 0.9399 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 1887 4.99 %RANDOM
Rwork0.1764 ---
obs0.1777 37841 --
Displacement parametersBiso max: 184.39 Å2 / Biso mean: 70.4771 Å2 / Biso min: 35.45 Å2
Baniso -1Baniso -2Baniso -3
1-4.1191 Å20 Å20 Å2
2--4.1191 Å20 Å2
3----8.2383 Å2
Refinement stepCycle: LAST / Resolution: 2.54→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7704 0 0 57 7761
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3632SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes175HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1177HARMONIC5
X-RAY DIFFRACTIONt_it7967HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1021SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9183SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7967HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10847HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion3.1
LS refinement shellResolution: 2.54→2.61 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2541 99 3.77 %
Rwork0.2239 2529 -
all0.2251 2628 -
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)
11.44190.21970.07091.05710.01611.4580.0277-0.2385-0.1064-0.0513-0.07740.00690.1128-0.13640.0497-0.12110.0212-0.00010.08610.0494-0.165513.5041-35.9126-135.837
22.8180.0788-0.19041.4974-0.2881.55660.0271-0.5156-0.05810.0143-0.089-0.1001-0.03410.10370.062-0.18180.02870.01880.09380.0314-0.247845.1991-24.3084-133.514
31.0845-0.1629-0.01370.85630.06340.864-0.05610.0069-0.0418-0.01080.04460.07060.0134-0.05480.01150.00330.03080.01570.01120.0174-0.125217.815-35.969-166.438
40.9099-0.37550.18170.96320.1371.0913-0.03770.04970.0909-0.0783-0.0089-0.0308-0.07070.0810.0467-0.01880.00920.021-0.00730.0324-0.101841.1119-11.6348-161.471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|246 }A3 - 246
2X-RAY DIFFRACTION2{ B|3 - B|195 B|199 - B|245 }B3 - 195
3X-RAY DIFFRACTION2{ B|3 - B|195 B|199 - B|245 }B199 - 245
4X-RAY DIFFRACTION3{ C|3 - C|196 C|199 - C|246 }C3 - 196
5X-RAY DIFFRACTION3{ C|3 - C|196 C|199 - C|246 }C199 - 246
6X-RAY DIFFRACTION4{ D|3 - D|245 }D3 - 245

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