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- PDB-3d33: Crystal structure of a duf3244 family protein with an immunoglobu... -

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Entry
Database: PDB / ID: 3d33
TitleCrystal structure of a duf3244 family protein with an immunoglobulin-like beta-sandwich fold (bvu_0276) from bacteroides vulgatus atcc 8482 at 1.70 A resolution
ComponentsDomain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyImmunoglobulin-like - #3080 / Protein of unknown function DUF3244 / Domain of unknown function (DUF3244) / Immunoglobulin-like / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesBacteroides vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold (YP_001297618.1) from Bacteroides vulgatus ATCC 8482 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: 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 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 1.4Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold
B: Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold


Theoretical massNumber of molelcules
Total (without water)23,8982
Polymers23,8982
Non-polymers00
Water5,098283
1
A: Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold


Theoretical massNumber of molelcules
Total (without water)11,9491
Polymers11,9491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold


Theoretical massNumber of molelcules
Total (without water)11,9491
Polymers11,9491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.562, 55.179, 47.116
Angle α, β, γ (deg.)90.000, 94.310, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: PRO / End label comp-ID: GLU / Refine code: 5 / Auth seq-ID: 34 - 134 / Label seq-ID: 8 - 108

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAUTHORS STATE THAT ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY (anSEC) SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold


Mass: 11948.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria)
Gene: YP_001297618.1, BVU_0276 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6KX32
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 28-134 OF THE FULL LENGTH PROTEIN. THIS REMOVED THE PUTATIVE SIGNAL PEPTIDE WHOSE PREDICTED CLEAVAGE SITE IS BETWEEN RESIDUES 28-29.

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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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.2000M MgFormate, 20.0000% PEG-3350, No Buffer pH 5.9, 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
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 11, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→28.677 Å / Num. obs: 25116 / % possible obs: 99.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 24.306 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.7470.8710.91232317630.87195.7
1.74-1.797.40.6961.11341518030.696100
1.79-1.847.40.551.41316317690.55100
1.84-1.97.50.4321.81267716980.432100
1.9-1.967.40.3352.21247616750.335100
1.96-2.037.40.252.91184015940.25100
2.03-2.117.40.2033.61136615300.203100
2.11-2.197.40.1774.11113614950.177100
2.19-2.297.40.1574.51060614250.157100
2.29-2.47.40.13951019413700.139100
2.4-2.537.50.1235.5971513030.123100
2.53-2.697.40.1056.3923312400.105100
2.69-2.877.50.0956.6863511560.095100
2.87-3.17.50.0847.6809910830.084100
3.1-3.47.50.0738.374409960.073100
3.4-3.87.50.0678.766948960.067100
3.8-4.397.40.0668.860178090.066100
4.39-5.387.30.0688.650046810.068100
5.38-7.67.10.0728.738075340.072100
7.6-28.686.70.0639.419792960.06397.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.7→28.677 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.951 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.104
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. THE FOLLOWING REGIONS ARE DISORDERED: A/B0, A/B28-33, A47-53, B46-53.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1283 5.1 %RANDOM
Rwork0.174 ---
obs0.176 25099 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.342 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0.05 Å2
2--0.32 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 0 283 1722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221532
X-RAY DIFFRACTIONr_bond_other_d0.0010.021019
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9772099
X-RAY DIFFRACTIONr_angle_other_deg0.84532516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2245205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.18825.15664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75815259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.805156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021708
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_nbd_refined0.1930.2235
X-RAY DIFFRACTIONr_nbd_other0.210.21061
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2712
X-RAY DIFFRACTIONr_nbtor_other0.0890.2876
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.180.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.219
X-RAY DIFFRACTIONr_mcbond_it1.91431033
X-RAY DIFFRACTIONr_mcbond_other0.5523391
X-RAY DIFFRACTIONr_mcangle_it2.71751579
X-RAY DIFFRACTIONr_scbond_it4.3748625
X-RAY DIFFRACTIONr_scangle_it5.98211509
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
553MEDIUM POSITIONAL0.120.5
664LOOSE POSITIONAL0.365
553MEDIUM THERMAL0.582
664LOOSE THERMAL1.1510
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 74 -
Rwork0.27 1685 -
all-1759 -
obs--95.44 %
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)
11.16270.31240.05691.77360.09212.39120.015-0.0750.00470.0108-0.0250.0761-0.00360.03410.01-0.06370.0074-0.0065-0.047-0.0074-0.04359.282511.724610.8684
21.2694-0.6028-0.42871.6648-0.11771.9261-0.00350.08040.0129-0.003-0.02440.0670.04340.05730.0278-0.0578-0.00950.0037-0.0388-0.0125-0.029210.612522.0998-9.3901
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA34 - 1348 - 108
2X-RAY DIFFRACTION2BB34 - 1348 - 108

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