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- PDB-3ljy: Crystal structure of putative adhesin (YP_001304413.1) from Parab... -

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Basic information

Entry
Database: PDB / ID: 3ljy
TitleCrystal structure of putative adhesin (YP_001304413.1) from Parabacteroides distasonis ATCC 8503 at 2.41 A resolution
Componentsputative adhesin
KeywordsCELL ADHESION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Lipoprotein / Adhesin
Function / homologyPectate Lyase C-like - #120 / Putative auto-transporter adhesin, head GIN domain / Putative auto-transporter adhesin, head GIN domain / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Putative auto-transporter adhesin head GIN domain-containing protein
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.41 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative adhesin (YP_001304413.1) from Parabacteroides distasonis ATCC 8503 at 2.41 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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
Revision 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative adhesin
B: putative adhesin
C: putative adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6379
Polymers78,0273
Non-polymers6106
Water2,504139
1
A: putative adhesin


Theoretical massNumber of molelcules
Total (without water)26,0091
Polymers26,0091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: putative adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2213
Polymers26,0091
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: putative adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4075
Polymers26,0091
Non-polymers3984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.951, 55.330, 120.613
Angle α, β, γ (deg.)90.000, 105.400, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 2 / Auth seq-ID: 23 - 260 / Label seq-ID: 4 - 241

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein putative adhesin


Mass: 26009.008 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_3085 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LGH7
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (21-262) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (21-262) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE 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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22.0000% polyethylene glycol 6000, 1.0000M lithium chloride, 0.1M TRIS 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: BL11-1 / Wavelength: 0.91837,0.97925,0.97876
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979251
30.978761
ReflectionResolution: 2.41→29.761 Å / Num. obs: 32190 / % possible obs: 98.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 53.817 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.41-2.472.20.5981.6445919950.59883.6
2.47-2.542.90.5112677923220.51198.4
2.54-2.6130.4092.6682522720.409100
2.61-2.6930.3053.3662222130.30599.9
2.69-2.7830.2494647521650.24999.8
2.78-2.8830.1985.1624420840.19899.7
2.88-2.9930.1745.8595119840.17499.8
2.99-3.1130.1377.3578419300.13799.8
3.11-3.2530.1089.6559418570.10899.6
3.25-3.4130.0912.2528617660.0999.6
3.41-3.5930.06715.7506716920.06799.5
3.59-3.8130.05618.2479215950.05699.4
3.81-4.0730.05218.9447914920.05299.1
4.07-4.430.04520.9416613920.04599
4.4-4.8230.03922.2388812910.03999.1
4.82-5.3930.03722.9353811780.03798.9
5.39-6.2230.04323.2307910290.04398.6
6.22-7.6230.04324.425588670.04398.4
7.62-10.782.90.03227.520416970.03298.3
10.78-29.772.80.02829.310163690.02893

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.41→29.761 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 16.34 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.386 / ESU R Free: 0.238
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (4). A CL ION FROM CRYSTALLIZATION CONDITION, AND PEG6000 OR PEG200 FRAGMENTS (PEG AND PGE) FROM CRYSTALLIZATION OR CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1628 5.1 %RANDOM
Rwork0.189 ---
obs0.191 32190 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.61 Å2 / Biso mean: 49.559 Å2 / Biso min: 20.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-0.25 Å2
2--1.33 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.41→29.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5303 0 39 139 5481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225546
X-RAY DIFFRACTIONr_bond_other_d0.0020.023560
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9497524
X-RAY DIFFRACTIONr_angle_other_deg0.90338851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2335742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.01826.756225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59815948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.239159
X-RAY DIFFRACTIONr_chiral_restr0.0870.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026292
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02969
X-RAY DIFFRACTIONr_nbd_refined0.2010.2707
X-RAY DIFFRACTIONr_nbd_other0.2040.23492
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22487
X-RAY DIFFRACTIONr_nbtor_other0.0850.23133
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2192
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.25
X-RAY DIFFRACTIONr_mcbond_it1.41133801
X-RAY DIFFRACTIONr_mcbond_other0.30531507
X-RAY DIFFRACTIONr_mcangle_it2.18145851
X-RAY DIFFRACTIONr_scbond_it2.96152050
X-RAY DIFFRACTIONr_scangle_it4.02861673
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1341TIGHT POSITIONAL0.060.05
2B1341TIGHT POSITIONAL0.040.05
3C1341TIGHT POSITIONAL0.050.05
1A1327MEDIUM POSITIONAL0.320.5
2B1327MEDIUM POSITIONAL0.310.5
3C1327MEDIUM POSITIONAL0.330.5
1A1341TIGHT THERMAL0.130.5
2B1341TIGHT THERMAL0.110.5
3C1341TIGHT THERMAL0.130.5
1A1327MEDIUM THERMAL0.82
2B1327MEDIUM THERMAL0.732
3C1327MEDIUM THERMAL0.792
LS refinement shellResolution: 2.41→2.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 96 -
Rwork0.269 1824 -
all-1920 -
obs--79.24 %
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)
13.103-0.88260.12451.4326-0.21711.2901-0.01940.09230.0641-0.01240.0715-0.0425-0.0769-0.0213-0.0521-0.09880.1880.0146-0.23060.0403-0.224715.471910.354519.4778
23.1088-0.1982-0.52521.70030.83564.88970.3477-0.07240.22870.2053-0.1431-0.1202-1.09010.7098-0.20460.4142-0.03090.0115-0.06140.0026-0.190824.15228.739545.7835
32.647-1.32950.28131.473-0.31451.4403-0.1003-0.1789-0.0991-0.06480.11160.04870.1325-0.0226-0.0113-0.10110.15350.0521-0.25590.0515-0.198126.381139.582113.3859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 261
2X-RAY DIFFRACTION2B23 - 260
3X-RAY DIFFRACTION3C23 - 261

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