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- PDB-3gf8: Crystal structure of putative polysaccharide binding proteins (DU... -

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Basic information

Entry
Database: PDB / ID: 3gf8
TitleCrystal structure of putative polysaccharide binding proteins (DUF1812) (NP_809975.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.20 A resolution
Componentsputative polysaccharide binding proteins (DUF1812)
KeywordsCarbohydrate Binding Protein / NP_809975.1 / putative polysaccharide binding proteins (DUF1812) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Lipoprotein / Unknown function
Function / homologyImmunoglobulin-like - #2090 / Immunoglobulin-like - #2100 / Fimbrium subunit FimB/Mfa2/Mfa3 / Fimbrillin-A associated anchor proteins Mfa1 and Mfa2 / cell outer membrane / Immunoglobulin-like / Sandwich / Mainly Beta / Putative lipoprotein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 A resolution
Authors: Xu, Q. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Cai, X. / Carlton, D. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ellrott, K. ...Authors: Xu, Q. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Cai, X. / Carlton, D. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ellrott, K. / Farr, C.L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Kumar, A. / Marciano, D. / McMullan, D. / Miller, M.D. / Morse, A.T. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Puckett, C. / Reyes, R. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Wooten, T. / Yeh, A. / Zhou, J. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
#1: Journal: Cell / Year: 2016
Title: A Distinct Type of Pilus from the Human Microbiome.
Authors: Xu, Q. / Shoji, M. / Shibata, S. / Naito, M. / Sato, K. / Elsliger, M.A. / Grant, J.C. / Axelrod, H.L. / Chiu, H.J. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Deacon, A.M. / Godzik, A. / ...Authors: Xu, Q. / Shoji, M. / Shibata, S. / Naito, M. / Sato, K. / Elsliger, M.A. / Grant, J.C. / Axelrod, H.L. / Chiu, H.J. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Curtis, M.A. / Nakayama, K. / Wilson, I.A.
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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 1.4Apr 22, 2020Group: Database references / Category: citation / citation_author
Revision 1.5Feb 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: putative polysaccharide binding proteins (DUF1812)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8382
Polymers34,7761
Non-polymers621
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.894, 106.894, 79.144
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein putative polysaccharide binding proteins (DUF1812)


Mass: 34776.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1062, NP_809975.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A8V5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 23-317) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 23-317) 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: 3.25 Å3/Da / Density % sol: 62.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.4M sodium citrate, 0.1 M HEPES pH 7.5, 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: 0.91162,0.97927,0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 9, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979271
30.979151
ReflectionResolution: 2.2→29.643 Å / Num. obs: 23862 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 35.684 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 6.793
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.2640.651.2701417450.65100
2.26-2.3240.5761.4675816820.576100
2.32-2.3940.4861.6658416440.486100
2.39-2.4640.4341.8641915960.434100
2.46-2.5440.3692.1624115540.369100
2.54-2.6340.3042.5602015050.304100
2.63-2.7340.2553.1581514460.255100
2.73-2.8440.2113.7559414030.211100
2.84-2.9740.1565543513550.156100
2.97-3.1140.1226.2509212780.122100
3.11-3.2840.0967.4492412410.096100
3.28-3.4840.0798.8464411700.079100
3.48-3.7240.06610.3436811040.066100
3.72-4.023.90.05711.3405110290.057100
4.02-4.43.90.0513.237539620.05100
4.4-4.923.90.04314.833988690.043100
4.92-5.683.80.04912.729817810.04999.9
5.68-6.963.80.05911.424826600.05999.8
6.96-9.843.60.05111.719165360.05199.6
9.84-29.653.30.04214.39903020.04294.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.643 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.07 / SU B: 9.773 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.171
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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. EDO MODELED IS PRESENT IN CRYO SOLUTION. 5. DENSITY FOR RESIDUES 220-229 ARE POOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1220 5.1 %RANDOM
Rwork0.189 ---
obs0.191 23827 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.51 Å2 / Biso mean: 32.216 Å2 / Biso min: 9.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2--1.14 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 4 174 2473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222378
X-RAY DIFFRACTIONr_bond_other_d0.0010.021569
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9453226
X-RAY DIFFRACTIONr_angle_other_deg0.84833822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8695293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06224.628121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9315414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0371512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022669
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02502
X-RAY DIFFRACTIONr_mcbond_it1.93531424
X-RAY DIFFRACTIONr_mcbond_other0.513583
X-RAY DIFFRACTIONr_mcangle_it3.2952299
X-RAY DIFFRACTIONr_scbond_it5.7718954
X-RAY DIFFRACTIONr_scangle_it7.77111922
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 95 -
Rwork0.238 1647 -
all-1742 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 8.0735 Å / Origin y: 30.3582 Å / Origin z: 26.3027 Å
111213212223313233
T0.0105 Å20.0052 Å2-0.0059 Å2-0.0122 Å2-0.0092 Å2--0.0099 Å2
L1.3728 °2-0.614 °2-0.2446 °2-0.7145 °20.1385 °2--0.6515 °2
S0.0841 Å °0.0373 Å °-0.0294 Å °-0.0422 Å °-0.0837 Å °0.0603 Å °0.0289 Å °0.01 Å °-0.0003 Å °

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