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- PDB-3fj1: Crystal structure of putative phosphosugar isomerase (YP_167080.1... -

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Basic information

Entry
Database: PDB / ID: 3fj1
TitleCrystal structure of putative phosphosugar isomerase (YP_167080.1) from SILICIBACTER POMEROYI DSS-3 at 1.75 A resolution
Componentsputative phosphosugar isomerase
KeywordsISOMERASE / YP_167080.1 / putative phosphosugar isomerase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Unknown function
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding
Similarity search - Function
GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSilicibacter pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative phosphosugar isomerase (YP_167080.1) from SILICIBACTER POMEROYI DSS-3 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 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 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 / 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 phosphosugar isomerase
B: putative phosphosugar isomerase
C: putative phosphosugar isomerase
D: putative phosphosugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,28216
Polymers145,8304
Non-polymers45212
Water21,8341212
1
A: putative phosphosugar isomerase
B: putative phosphosugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1548
Polymers72,9152
Non-polymers2396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-65 kcal/mol
Surface area22630 Å2
MethodPISA
2
C: putative phosphosugar isomerase
D: putative phosphosugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1288
Polymers72,9152
Non-polymers2136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-80 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.400, 114.141, 197.279
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A0 - 331
2115B0 - 331
3115C0 - 331
4115D0 - 331
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUGGESTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
putative phosphosugar isomerase / SIS domain protein


Mass: 36457.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi DSS-3 (bacteria) / Gene: SPO1843, YP_167080.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LSC5
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 1212 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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.

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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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.2000M MgCl2, 20.0000% PEG-3350, No Buffer pH 5.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97967
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979671
ReflectionResolution: 1.75→29.386 Å / Num. obs: 117679 / % possible obs: 98.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 16.07 Å2 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.128 / Rsym value: 0.115 / Net I/av σ(I): 4.888 / Net I/σ(I): 9.4 / Num. measured all: 506838
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.75-1.82.70.5961.21981972900.7070.5961.783.4
1.8-1.843.50.5081.42887283400.5950.5082.497.6
1.84-1.93.60.4161.82946082230.4850.416398.9
1.9-1.963.60.3422.22887380070.3990.3423.699
1.96-2.023.60.2632.82853678300.3070.2634.699.3
2.02-2.093.60.23432758975630.2730.2345.299.5
2.09-2.173.70.18542670672950.2150.1856.499.6
2.17-2.263.60.1673.42562670290.1950.1677.399.7
2.26-2.363.60.1484.82463667840.1720.1488.399.8
2.36-2.473.60.1335.22348965010.1550.1339.399.8
2.47-2.613.60.1156.12244261840.1340.11510.299.8
2.61-2.773.70.0947.42149658700.1090.09411.799.8
2.77-2.963.70.08582043754930.0990.08513.499.7
2.96-3.270.1494.43590551440.1610.14915.899.8
3.2-3.57.20.125.53439147830.130.1218.499.7
3.5-3.917.20.0946.93098243000.1020.09421.699.7
3.91-4.527.10.087.42685038080.0860.0824.499.5
4.52-5.5370.0718.92287432520.0770.07125.399
5.53-7.837.10.0788.11805425510.0840.07823.498.7
7.83-29.396.80.05210.3980114320.0560.05225.395.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→29.386 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.471 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.111
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). CHLORIDE ANIONS FROM THE CRYSTALLIZATION SOLUTION AND AN ETHYLENE GLYCOL USED AS ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.(2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY (3). CHLORIDE ANIONS FROM THE CRYSTALLIZATION SOLUTION AND AN ETHYLENE GLYCOL USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 5897 5 %RANDOM
Rwork0.162 111709 --
obs0.164 117606 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.88 Å2 / Biso mean: 14.586 Å2 / Biso min: 3.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.44 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9647 0 15 1212 10874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210222
X-RAY DIFFRACTIONr_bond_other_d0.0020.026822
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9713996
X-RAY DIFFRACTIONr_angle_other_deg1.042316639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.06151425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.09422.336411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.398151626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.215108
X-RAY DIFFRACTIONr_chiral_restr0.0960.21672
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211747
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022121
X-RAY DIFFRACTIONr_nbd_refined0.2180.32166
X-RAY DIFFRACTIONr_nbd_other0.1920.37477
X-RAY DIFFRACTIONr_nbtor_refined0.170.55105
X-RAY DIFFRACTIONr_nbtor_other0.0880.55100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.51626
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.321
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.3130
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.572
X-RAY DIFFRACTIONr_mcbond_it0.75226899
X-RAY DIFFRACTIONr_mcbond_other0.20522728
X-RAY DIFFRACTIONr_mcangle_it1.164310803
X-RAY DIFFRACTIONr_scbond_it0.86823646
X-RAY DIFFRACTIONr_scangle_it1.30633137
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1859MEDIUM POSITIONAL0.20.5
2B1859MEDIUM POSITIONAL0.170.5
3C1859MEDIUM POSITIONAL0.160.5
4D1859MEDIUM POSITIONAL0.180.5
1A1750LOOSE POSITIONAL0.525
2B1750LOOSE POSITIONAL0.445
3C1750LOOSE POSITIONAL0.595
4D1750LOOSE POSITIONAL0.635
1A1859MEDIUM THERMAL0.862
2B1859MEDIUM THERMAL1.042
3C1859MEDIUM THERMAL0.92
4D1859MEDIUM THERMAL1.012
1A1750LOOSE THERMAL1.2110
2B1750LOOSE THERMAL1.3710
3C1750LOOSE THERMAL1.3210
4D1750LOOSE THERMAL1.3710
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 372 -
Rwork0.252 6878 -
all-7250 -
obs--82.6 %
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)
10.17920.05890.08430.38290.14760.3242-0.00930.0061-0.0123-0.0132-0.0016-0.00940.08940.0310.01080.0350.011-0.0112-0.006-0.00870.007136.08342.9563.996
20.31270.0391-0.2360.29820.07610.70250.0170.02420.0181-0.03150.002-0.0153-0.0360.0058-0.0190.00230.003-0.0039-0.0074-0.0041-0.001236.84571.1121.265
30.3743-0.18430.2370.4548-0.16930.31520.04120.0283-0.042-0.04390.00460.06080.01530.0139-0.04580.01720.008-0.01450.0020.0121-0.006211.4337.07552.37
40.24020.1335-0.16130.3628-0.19840.52450.0425-0.00410.03480.05010.00880.0705-0.08610.0088-0.05130.02170.0030.0226-0.00470.00080.012815.50564.5353.312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 331
2X-RAY DIFFRACTION2B4 - 331
3X-RAY DIFFRACTION3C5 - 331
4X-RAY DIFFRACTION4D1 - 332

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