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- PDB-1z6n: 1.5 A Crystal Structure of a Protein of Unknown Function PA1234 f... -

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Basic information

Entry
Database: PDB / ID: 1z6n
Title1.5 A Crystal Structure of a Protein of Unknown Function PA1234 from Pseudomonas aeruginosa
Componentshypothetical protein PA1234
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pseudomonas aeruginosa / alpha-beta-alpha sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyThioredoxin / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Thioredoxin family protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsZhang, R. / Xu, L. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.5A crystal structure of a hypothetical protein PA1234 from Pseudomonas aeruginosa
Authors: Zhang, R. / Xu, L. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMar 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PA1234
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5042
Polymers18,4801
Non-polymers241
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.686, 75.818, 90.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-306-

HOH

31A-331-

HOH

41A-436-

HOH

DetailsThis protein existed as monomer. The deposited coords. represent the monomer in the asymmtric unit.

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Components

#1: Protein hypothetical protein PA1234


Mass: 18480.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: gi:15596431 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I4A4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.412 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 0.2 M MgCl2, 28% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9797 Å
DetectorType: SBC-2 / Detector: CCD / Date: Nov 29, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 27878 / Num. obs: 27153 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 15.682 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.88
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.72 / Num. unique all: 2744 / % possible all: 83.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→58.22 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.083
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22047 1365 5 %RANDOM
Rwork0.18902 ---
all0.19058 26480 --
obs0.19058 25787 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.682 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---0.33 Å20 Å2
3---1.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.082 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.083 Å
Refinement stepCycle: LAST / Resolution: 1.5→58.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 1 257 1547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221309
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.981770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8655165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49723.63666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93615222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6351514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021009
X-RAY DIFFRACTIONr_nbd_refined0.1930.2667
X-RAY DIFFRACTIONr_nbtor_refined0.310.2901
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2222
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.245
X-RAY DIFFRACTIONr_mcbond_it0.751.5844
X-RAY DIFFRACTIONr_mcangle_it1.20321300
X-RAY DIFFRACTIONr_scbond_it2.0013513
X-RAY DIFFRACTIONr_scangle_it3.2334.5470
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 93 -
Rwork0.279 1527 -
obs--79.8 %
Refinement TLS params.Method: refined / Origin x: 10.4643 Å / Origin y: 12.2265 Å / Origin z: 33.0186 Å
111213212223313233
T-0.0459 Å2-0.0225 Å2-0.0291 Å2--0.0411 Å20.0562 Å2---0.0124 Å2
L1.4213 °2-0.3068 °20.0268 °2-2.2505 °2-0.7443 °2--0.784 °2
S-0.01 Å °0.0322 Å °0.2365 Å °0.0771 Å °-0.1786 Å °-0.3909 Å °-0.1184 Å °0.0976 Å °0.1887 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 331 - 33
2X-RAY DIFFRACTION1AA34 - 6034 - 60
3X-RAY DIFFRACTION1AA61 - 10661 - 106
4X-RAY DIFFRACTION1AA107 - 136107 - 136
5X-RAY DIFFRACTION1AA137 - 149137 - 149
6X-RAY DIFFRACTION1AA150 - 166150 - 166

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