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- PDB-3n6y: Crystal structure of an immunoglobulin-like protein (PA1606) from... -

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Basic information

Entry
Database: PDB / ID: 3n6y
TitleCrystal structure of an immunoglobulin-like protein (PA1606) from PSEUDOMONAS AERUGINOSA at 1.50 A resolution
Componentsimmunoglobulin-like protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyImmunoglobulin-like - #2390 / Domain of unknown function DUF3859 / Domain of unknown function (DUF3859) / Immunoglobulin-like / Sandwich / Mainly Beta / DUF3859 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an immunoglobulin-like protein (PA1606) from PSEUDOMONAS AERUGINOSA at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: immunoglobulin-like protein
B: immunoglobulin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6434
Polymers31,3522
Non-polymers2902
Water6,738374
1
A: immunoglobulin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8702
Polymers15,6761
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: immunoglobulin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7722
Polymers15,6761
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-13 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.073, 65.341, 53.065
Angle α, β, γ (deg.)90.000, 103.190, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein immunoglobulin-like protein


Mass: 15676.153 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA1606 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9I3B5
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 23-158) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 23-158) 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.200000000M Na2SO4, 20.000000000% PEG-3350, No Buffer pH 6.6, 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: 0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.5→28.621 Å / Num. obs: 43788 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 14.951 Å2 / Rsym value: 0.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0073refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.3.15data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→28.621 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.634 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.08
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. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. SULFATE (SO4) ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. SULFATE (SO4) ION AND PEG-200 (PG4) FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2199 5 %RANDOM
Rwork0.181 ---
obs0.182 43740 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 114.25 Å2 / Biso mean: 22.887 Å2 / Biso min: 11.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å20 Å2-0.32 Å2
2---1.1 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 15 374 2319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222202
X-RAY DIFFRACTIONr_bond_other_d0.0010.021550
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9833018
X-RAY DIFFRACTIONr_angle_other_deg0.80333821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.23524.779113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98915402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2741516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212502
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02436
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 157 -
Rwork0.277 3059 -
all-3216 -
obs--99.81 %
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)
12.31731.19793.22331.07962.00355.3492-0.0432-0.24460.16920.035-0.13510.1417-0.2129-0.41320.17820.07840.01770.0060.1206-0.00250.124221.942419.180737.9207
229.416520.052810.825337.245721.534616.6421-0.51882.05431.6017-1.77610.2543-0.0335-1.28051.5340.26440.2776-0.03220.00170.70690.290.281922.66823.88718.9523
30.35660.14830.1391.10990.04951.04990.03940.01130.0638-0.0021-0.03120.0267-0.037-0.0566-0.00810.00820.01250.01110.07510.00980.066524.334710.929728.8881
40.28220.20890.23310.85490.15351.32320.03440.00910.0147-0.0507-0.0189-0.02790.03390.0274-0.01550.01330.01090.00340.0690.00110.069326.44756.758628.4051
51.265-0.12551.85650.6728-0.79056.86370.0768-0.12240.0287-0.0059-0.04060.0985-0.0609-0.4049-0.03620.02440.00880.01170.08320.00840.087918.03048.137833.4761
625.2868-13.523-7.98057.2344.26742.51980.61031.31610.0591-0.2833-0.6456-0.0389-0.1864-0.40680.03530.24930.05250.01920.2482-0.01090.203634.5318-19.317427.3081
71.7831-0.5783-1.0242.46760.91342.1578-0.0044-0.0638-0.15510.1305-0.02030.09950.2392-0.05520.02480.0592-0.043-0.01880.07340.01950.082715.6802-16.771145.2254
80.5114-0.7658-0.76772.35890.42061.70810.0229-0.01880.05380.0694-0.0136-0.15620.03060.0562-0.00940.1094-0.0128-0.00950.1074-0.01010.104926.4672-4.838843.1132
92.5992-2.26490.65812.30621.22540.48150.0547-0.21170.06420.2804-0.0231-0.43720.0693-0.0902-0.03160.14740.0475-0.00880.13150.00070.094533.5775-16.708341.0919
100.6644-0.1466-0.49190.8963-0.39181.68060.03160.0398-0.00370.06070.03050.07080.0491-0.1303-0.06210.023-0.0158-0.00180.0530.00060.062118.8751-6.985943.1604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 38
2X-RAY DIFFRACTION2A39 - 58
3X-RAY DIFFRACTION3A59 - 103
4X-RAY DIFFRACTION4A104 - 145
5X-RAY DIFFRACTION5A146 - 158
6X-RAY DIFFRACTION6B0 - 28
7X-RAY DIFFRACTION7B29 - 77
8X-RAY DIFFRACTION8B78 - 110
9X-RAY DIFFRACTION9B111 - 120
10X-RAY DIFFRACTION10B121 - 158

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