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- PDB-4pux: Crystal structure of a beta-barrel like protein (ABAYE2633) from ... -

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Basic information

Entry
Database: PDB / ID: 4pux
TitleCrystal structure of a beta-barrel like protein (ABAYE2633) from Acinetobacter baumannii AYE at 1.43 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta-barrel fold / PF11578 family / DUF3237 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyUncharacterised protein family UPF0311 / Protein of unknown function (DUF3237) / Porin - #20 / Porin / Beta Barrel / Mainly Beta / CITRIC ACID / UPF0311 protein ABAYE2633
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.43 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (ABAYE2633) from Acinetobacter baumannii AYE at 1.43 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 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

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,46611
Polymers17,8481
Non-polymers61810
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,86244
Polymers71,3924
Non-polymers2,47140
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area18060 Å2
ΔGint-172 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.338, 99.178, 48.677
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-210-

CL

21A-402-

HOH

31A-465-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 17847.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AYE / Gene: ABAYE2633 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B0VAD0
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 20-178 OF 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.0M lithium chloride, 20.0% polyethylene glycol 6000, 0.1M citric acid pH 4.0, 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: 0.91837,0.9798,0.97913
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97981
30.979131
ReflectionResolution: 1.43→24.978 Å / Num. obs: 27406 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.239 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 12.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.43-1.480.3422.28441491595.4
1.48-1.540.24639018517596.1
1.54-1.610.1864.18635505795.3
1.61-1.70.1395.39147532294.6
1.7-1.80.0967.58459480296.4
1.8-1.940.06510.58563501993.8
1.94-2.140.04415.39051515495.5
2.14-2.440.03319.98631488294.4
2.44-3.080.02724.49170512795.6
3.080.01932.58865498293.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMAC5.8.0049refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.43→24.978 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.088 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.055
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. 1,2-ETHANE-DIOL(EDO), CHLORIDE(CL) AND CITRATE(CIT) MODELED WERE PRESENT IN CRYSTALLIZATION OR CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1528 1378 5 %RANDOM
Rwork0.1181 ---
obs0.1199 27406 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.98 Å2 / Biso mean: 19.2014 Å2 / Biso min: 7.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.43→24.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1233 0 34 212 1479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221377
X-RAY DIFFRACTIONr_bond_other_d0.0020.021360
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9951878
X-RAY DIFFRACTIONr_angle_other_deg0.82733158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1924.46456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94715252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.331157
X-RAY DIFFRACTIONr_chiral_restr0.1150.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211555
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02295
X-RAY DIFFRACTIONr_mcbond_it2.7481.359662
X-RAY DIFFRACTIONr_mcbond_other2.7181.356661
X-RAY DIFFRACTIONr_mcangle_it3.262.049833
X-RAY DIFFRACTIONr_rigid_bond_restr3.16332737
X-RAY DIFFRACTIONr_sphericity_free30.2725161
X-RAY DIFFRACTIONr_sphericity_bonded9.69452766
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 87 -
Rwork0.204 1903 -
all-1990 -
obs--98.47 %

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