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- PDB-4e72: Crystal structure of a DUF3298 family protein (PA4972) from Pseud... -

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Basic information

Entry
Database: PDB / ID: 4.0E+72
TitleCrystal structure of a DUF3298 family protein (PA4972) from Pseudomonas aeruginosa PAO1 at 2.15 A resolution
Componentsuncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF11738 FAMILY / DUF3298 / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


Fervidobacterium nodosum Rt17-B1 like / Heat-shock cognate protein, ATPase / Domain of unknown function DUF3298 / PdaC/RsiV-like superfamily / Protein of unknown function (DUF3298) / Actin; Chain A, domain 4 / Heat Shock Protein 90 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DUF3298 domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (PA4972) from Pseudomonas aeruginosa PAO1 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Structure summary
Revision 1.2Dec 24, 2014Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Feb 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
Revision 1.6Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)25,6191
Polymers25,6191
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.840, 51.890, 40.860
Angle α, β, γ (deg.)90.000, 98.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein uncharacterized protein


Mass: 25618.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4972 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9HUJ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 24-248) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 24-248) 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10.0% Glycerol, 1.26M tri-Sodium Citrate, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9796,0.9184
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 29, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.91841
ReflectionResolution: 2.15→46.229 Å / Num. obs: 11243 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.47 % / Biso Wilson estimate: 36.721 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.15-2.233.120.4392.433363107890.9
2.23-2.320.3633.44018112097.1
2.32-2.420.29243852108697.4
2.42-2.550.2264.74120116597.6
2.55-2.710.17163869111296.9
2.71-2.920.1247.53789111994.6
2.92-3.210.08810.84123113998.7
3.21-3.670.07314.13989113697
3.67-4.610.06216.53743110594.6
4.61-46.230.05917.94094118395.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.15→46.229 Å / Cor.coef. Fo:Fc: 0.9449 / Cor.coef. Fo:Fc free: 0.916 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 532 4.74 %RANDOM
Rwork0.1713 ---
obs0.1732 11219 96.02 %-
Displacement parametersBiso max: 142.33 Å2 / Biso mean: 43.9958 Å2 / Biso min: 20.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.5077 Å20 Å21.7381 Å2
2---10.351 Å20 Å2
3---9.8433 Å2
Refine analyzeLuzzati coordinate error obs: 0.264 Å
Refinement stepCycle: LAST / Resolution: 2.15→46.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 0 50 1781
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d813SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes262HARMONIC5
X-RAY DIFFRACTIONt_it1799HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion223SEMIHARMONIC5
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_contact1936SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1799HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2454HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion2.89
LS refinement shellResolution: 2.15→2.35 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2361 113 4.32 %
Rwork0.1846 2503 -
all0.1869 2616 -
obs--96.02 %
Refinement TLS params.Method: refined / Origin x: 35.8035 Å / Origin y: 17.934 Å / Origin z: 18.4987 Å
111213212223313233
T-0.1395 Å20.0041 Å2-0.0137 Å2-0.0231 Å20.0197 Å2---0.1317 Å2
L1.0421 °20.1792 °20.1769 °2-1.3059 °20.4648 °2--2.0653 °2
S-0.0736 Å °-0.1913 Å °-0.0596 Å °-0.0369 Å °0.0571 Å °-0.0681 Å °0.0407 Å °0.0489 Å °0.0165 Å °
Refinement TLS groupSelection details: { A|26 - 247 }

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