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- PDB-3sb3: Crystal structure of an apag protein (PA1934) from pseudomonas ae... -

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Basic information

Entry
Database: PDB / ID: 3sb3
TitleCrystal structure of an apag protein (PA1934) from pseudomonas aeruginosa pao1 at 1.83 A resolution
ComponentsApaG protein
KeywordsStructural Genomics / Unknown Function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF4354 / Protein of unknown function DUF4354 / Domain of unknown function (DUF4354) / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION / DUF4354 family protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an ApaG protein (PA1934) from PSEUDOMONAS AERUGINOSA at 1.83 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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 1.6Nov 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: ApaG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2912
Polymers11,1961
Non-polymers951
Water1,38777
1
A: ApaG protein
hetero molecules

A: ApaG protein
hetero molecules

A: ApaG protein
hetero molecules

A: ApaG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1658
Polymers44,7854
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area5110 Å2
ΔGint-29 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.080, 66.080, 50.538
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-127-

PO4

21A-127-

PO4

DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT THE TETRAMER IS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein ApaG protein


Mass: 11196.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA1934 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9I2H0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 22-126) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 22-126) 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 30.00% PEG-400, 0.1M TRIS pH 8.5, 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: 0.91837,0.97936,0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 12, 2010 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979361
30.97921
ReflectionResolution: 1.83→29.552 Å / Num. obs: 10313 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.69 % / Biso Wilson estimate: 27.998 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.83-1.90.791.867786191094.5
1.9-1.970.5462.87237172099.8
1.97-2.060.3244.77989188799.9
2.06-2.170.2436.38144192999.8
2.17-2.310.1718.68206194399.8
2.31-2.480.13211.47582178199.9
2.48-2.730.0861680981898100
2.73-3.130.04826.58255193099.9
3.13-3.930.02744.379351867100
3.930.02156.98061191099.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 30, 2009data scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.83→29.552 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.199 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3 .A MET-INHIBITION ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 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.SOLVENT MOLECULES WERE EXCLUDED FROM THE ASSIGNMENT OF THE TLS GROUPS. 5. BASED ON FIT TO ELECTRON DENSITY, A PHOSPHATE (PO4) HAS BEEN MODELED AT A SPECIAL POSITION NEAR THE SIDECHAINS OF ARG 124 AND ARG 120. HOWEVER, THIS ASSIGNMENT OF ELECTRON DENSITY TO A PHOSPHATE IS TENTATIVE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 497 4.8 %RANDOM
Rwork0.1872 ---
obs0.1888 10296 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.72 Å2 / Biso mean: 30.2006 Å2 / Biso min: 16.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.83→29.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms730 0 5 77 812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022782
X-RAY DIFFRACTIONr_bond_other_d0.0030.02507
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9561068
X-RAY DIFFRACTIONr_angle_other_deg0.97831243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76824.41234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06115127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.415156
X-RAY DIFFRACTIONr_chiral_restr0.1080.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02913
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02161
X-RAY DIFFRACTIONr_mcbond_it1.0981.5519
X-RAY DIFFRACTIONr_mcbond_other0.3291.5214
X-RAY DIFFRACTIONr_mcangle_it1.8942831
X-RAY DIFFRACTIONr_scbond_it3.0923263
X-RAY DIFFRACTIONr_scangle_it5.3044.5232
LS refinement shellResolution: 1.831→1.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 50 -
Rwork0.266 671 -
all-721 -
obs--96.78 %
Refinement TLS params.Method: refined / Origin x: 29.3913 Å / Origin y: 19.1675 Å / Origin z: 15.1368 Å
111213212223313233
T0.0352 Å20.0101 Å20.0001 Å2-0.0281 Å20.0032 Å2--0.0488 Å2
L1.7539 °2-0.6452 °2-0.2102 °2-0.0267 °20.2994 °2--0.4807 °2
S0.0568 Å °0.1491 Å °0.0185 Å °0.0473 Å °-0.0448 Å °-0.0611 Å °-0.0751 Å °-0.0616 Å °-0.012 Å °

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