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- PDB-4kw2: Crystal structure of a Putative uncharacterized protein (BDI_1873... -

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Basic information

Entry
Database: PDB / ID: 4kw2
TitleCrystal structure of a Putative uncharacterized protein (BDI_1873) from Parabacteroides distasonis ATCC 8503 at 2.32 A resolution
ComponentsUncharacterized protein
KeywordsISOMERASE / Xylose isomerase-like TIM barrel / PF01261 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology: / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Xylose isomerase-like TIM barrel domain-containing protein
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.32 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative uncharacterized protein (BDI_1873) from Parabacteroides distasonis ATCC 8503 at 2.32 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4109
Polymers30,6761
Non-polymers7358
Water1,49583
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,23127
Polymers92,0283
Non-polymers2,20424
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation30_555z,-x+1/2,-y+1/21
crystal symmetry operation84_555-y+1/2,-z+1/2,x1
Buried area6040 Å2
ΔGint-21 kcal/mol
Surface area30220 Å2
MethodPISA
2
A: Uncharacterized protein
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)376,926108
Polymers368,11212
Non-polymers8,81496
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation28_555x,-y+1/2,-z+1/21
crystal symmetry operation30_555z,-x+1/2,-y+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation51_555-x+1/2,y,-z+1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation74_555-x+1/2,-y+1/2,z1
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
crystal symmetry operation84_555-y+1/2,-z+1/2,x1
Buried area34010 Å2
ΔGint-59 kcal/mol
Surface area111050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.095, 200.095, 200.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

21A-302-

SO4

31A-418-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TRIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 30675.986 Da / Num. of mol.: 1 / Fragment: UNP residues 26-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_1873 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LD44
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY RESIDUES 26- ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY RESIDUES 26-271 OF 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: 54.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.19
Details: 1.48M ammonium sulfate, 0.1M phosphate-citrate pH 4.19, Additive 0.005 M Myo-Inositol, 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: 0.8434,0.9787,0.96911
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.84341
20.97871
30.969111
ReflectionResolution: 2.32→28.881 Å / Num. all: 15409 / Num. obs: 15409 / % possible obs: 100 % / Redundancy: 35.8 % / Biso Wilson estimate: 42.539 Å2 / Rsym value: 0.316 / Net I/σ(I): 13.7
Reflection shell

Rmerge(I) obs: 0.026 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.32-2.3836.40.34002611002.643100
2.38-2.4538.20.34148110872.169100
2.45-2.52380.43999710531.858100
2.52-2.5937.60.53817410161.62100
2.59-2.6837.30.5367259851.414100
2.68-2.7736.80.7361639831.128100
2.77-2.8836.30.9335779250.813100
2.88-330.91.2279339030.647100
3-3.1334.61.6297158600.468100
3.13-3.2838.82.1326998420.353100
3.28-3.4637.92.9299417900.257100
3.46-3.67373.5282227620.211100
3.67-3.9236.54.3256627040.173100
3.92-4.2433.35.9225356770.123100
4.24-4.6429.26.8180156180.106100
4.64-5.1937.16.7212315730.104100
5.19-5.9936.15.5182805070.132100
5.99-7.3432.35.5145204490.129100
7.34-10.3828.18.2100183570.079100
10.38-28.88131.88.569242180.06895.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.32→28.881 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 11.256 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.195
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. SULFATE (SO4) AND ETHYLENE GLYCOL (EDO) FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 781 5.1 %RANDOM
Rwork0.1829 ---
obs0.1847 15408 99.85 %-
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: 139.88 Å2 / Biso mean: 46.5994 Å2 / Biso min: 22.03 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.32→28.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 39 83 2032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192022
X-RAY DIFFRACTIONr_bond_other_d0.0010.021878
X-RAY DIFFRACTIONr_angle_refined_deg0.9771.9682743
X-RAY DIFFRACTIONr_angle_other_deg0.69634329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2765248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.10524.79698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17315330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.889158
X-RAY DIFFRACTIONr_chiral_restr0.0620.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022269
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02471
X-RAY DIFFRACTIONr_mcbond_it2.7356.854968
X-RAY DIFFRACTIONr_mcbond_other2.7066.844967
X-RAY DIFFRACTIONr_mcangle_it4.47212.7791209
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 68 -
Rwork0.256 1024 -
all-1092 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: 78.761 Å / Origin y: 23.249 Å / Origin z: 53.236 Å
111213212223313233
T0.046 Å20.0135 Å20.0119 Å2-0.0966 Å2-0.0058 Å2--0.1014 Å2
L1.0629 °20.7802 °20.267 °2-1.2011 °2-0.0911 °2--0.6399 °2
S0.0047 Å °0.0703 Å °-0.1721 Å °0.0275 Å °0.0132 Å °-0.1658 Å °-0.0356 Å °0.1377 Å °-0.0179 Å °

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