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- PDB-3kdw: Crystal structure of Putative sugar binding protein (YP_001300177... -

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Basic information

Entry
Database: PDB / ID: 3kdw
TitleCrystal structure of Putative sugar binding protein (YP_001300177.1) from Bacteroides vulgatus ATCC 8482 at 1.70 A resolution
ComponentsPutative sugar binding protein
KeywordsSUGAR BINDING PROTEIN / Putative sugar binding protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyProtein of unknown function DUF3826 / Protein of unknown function (DUF3826) / PHOSPHATE ION / DUF3826 domain-containing protein
Function and homology information
Biological speciesBacteroides vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative sugar binding protein (YP_001300177.1) from Bacteroides vulgatus ATCC 8482 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,64012
Polymers25,5851
Non-polymers1,05511
Water4,558253
1
A: Putative sugar binding protein
hetero molecules

A: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,28024
Polymers51,1702
Non-polymers2,11022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area9990 Å2
ΔGint-192 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.303, 75.303, 87.128
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative sugar binding protein


Mass: 25585.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria)
Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_2916 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6L4E1

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Non-polymers , 5 types, 264 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE CRYSTALLIZATION REAGENT CONTAINED A RACEMIC MIXTURE (4R/4S) OF 2-METHYL-2,4-PENTANEDIOL (MPD) ...THE CRYSTALLIZATION REAGENT CONTAINED A RACEMIC MIXTURE (4R/4S) OF 2-METHYL-2,4-PENTANEDIOL (MPD) ONE OF THE SOLVENT SITES HAS BEEN MODELED AS MIXTURE OF BOTH ENANTIOMERS RESID 301 (4S - MPD) AND RESID 302 (4R - MRD).
Sequence detailsSEQUENCE THIS CONSTRUCT (RESIDUES 21-222) WAS EXPRESSED WITH THE N-TERMINAL PURIFICATION TAG ...SEQUENCE THIS CONSTRUCT (RESIDUES 21-222) WAS EXPRESSED WITH THE N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M (NH4)2HPO4, 50.0000% MPD, 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: BL11-1 / Wavelength: 0.91837,0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 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
20.979291
ReflectionResolution: 1.7→28.49 Å / Num. obs: 31900 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.086 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.69
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.760.552166595898198
1.76-1.830.412.7172916063199.7
1.83-1.910.2983.6166555827199.7
1.91-2.020.1836189866622199.6
2.02-2.140.1129.3164205720199.6
2.14-2.310.07513.5179666237199.7
2.31-2.540.05318.3172465967199.6
2.54-2.90.03625.4174606020199.7
2.9-3.660.02437.2177686115199.7
3.66-28.490.01948.6176796080199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→28.49 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.124 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.086
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 PROTEIN ...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. CHLORIDE (CL), (4S)-2-METHYL-2,4-PENTANEDIOL (MPD) (4R)-2-METHYL-2,4-PENTANEDIOL (MRD), AND PHOSPHATE (PO4) FROM THE PROTEIN/CRYSTALLIZATION SOLUTION HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 5. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1609 5 %RANDOM
Rwork0.152 ---
obs0.154 31866 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.56 Å2 / Biso mean: 14.705 Å2 / Biso min: 4.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.09 Å20 Å2
2---0.19 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1626 0 60 253 1939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221831
X-RAY DIFFRACTIONr_bond_other_d0.0010.021246
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9882508
X-RAY DIFFRACTIONr_angle_other_deg1.04133043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4565244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23924.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21715333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3211515
X-RAY DIFFRACTIONr_chiral_restr0.0970.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022044
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02377
X-RAY DIFFRACTIONr_mcbond_it0.8271.51085
X-RAY DIFFRACTIONr_mcbond_other0.2841.5439
X-RAY DIFFRACTIONr_mcangle_it1.50421759
X-RAY DIFFRACTIONr_scbond_it2.5283746
X-RAY DIFFRACTIONr_scangle_it3.9864.5728
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 114 -
Rwork0.264 2172 -
all-2286 -
obs--97.86 %
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)
110.55271.7724-4.11170.74550.29713.87080.05420.66560.0022-0.03040.0939-0.0562-0.1502-0.1741-0.14810.10450.01350.03730.22060.01160.154234.51728.52422.772
22.8787-0.0050.22165.66070.27681.67190.00780.40840.0918-0.5509-0.12550.0745-0.047-0.12350.11780.07980.01020.02040.20480.0370.057425.32231.64221.173
34.69031.8711-1.11041.813-0.69191.2201-0.10870.3367-0.2945-0.15420.07610.04270.1778-0.18670.03260.0576-0.0179-0.0020.1094-0.0370.116515.61922.35230.776
41.1158-0.6911-0.11220.6134-0.04481.09760.02670.09010.1419-0.0152-0.0087-0.049-0.1777-0.0329-0.0180.0860.0008-0.00520.09510.01560.122514.22939.48236.575
51.8244-1.22250.90785.1178-1.42821.4097-0.1812-0.03870.2145-0.17210.20470.0878-0.1655-0.0546-0.02340.12440.0403-0.01320.05170.01630.1322-1.46553.87935.141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 25
2X-RAY DIFFRACTION2A26 - 49
3X-RAY DIFFRACTION3A50 - 98
4X-RAY DIFFRACTION4A99 - 189
5X-RAY DIFFRACTION5A190 - 220

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