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- PDB-3knz: Crystal structure of Putative sugar binding protein (NP_459565.1)... -

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Basic information

Entry
Database: PDB / ID: 3knz
TitleCrystal structure of Putative sugar binding protein (NP_459565.1) from Salmonella typhimurium LT2 at 2.50 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 / homology
Function and homology information


glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / carbohydrate derivative binding / protein N-linked glycosylation / fructose 6-phosphate metabolic process
Similarity search - Function
GlmS/FrlB, SIS domain 2 / GlmS/AgaS, SIS domain 1 / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-ETHOXYETHANOL / IMIDAZOLE / Inner membrane protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative sugar binding protein (NP_459565.1) from Salmonella typhimurium LT2 at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative sugar binding protein
B: Putative sugar binding protein
C: Putative sugar binding protein
D: Putative sugar binding protein
E: Putative sugar binding protein
F: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,26110
Polymers246,9426
Non-polymers3184
Water7,764431
1
A: Putative sugar binding protein
B: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4734
Polymers82,3142
Non-polymers1592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-5 kcal/mol
Surface area25370 Å2
MethodPISA
2
C: Putative sugar binding protein
D: Putative sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4734
Polymers82,3142
Non-polymers1592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint0 kcal/mol
Surface area25320 Å2
MethodPISA
3
E: Putative sugar binding protein
F: Putative sugar binding protein


Theoretical massNumber of molelcules
Total (without water)82,3142
Polymers82,3142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-13 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.028, 173.344, 208.574
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
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A-3 - 321
2114B-3 - 321
3114C-3 - 321
4114D-3 - 321
5114E-3 - 321
6114F-3 - 321
DetailsCRYSTAL PACKING ANALYSIS AND SIZE EXCLUSION CHROMATOGRAPHY COMBINED WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein
Putative sugar binding protein / Putative inner membrane protein


Mass: 41157.023 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: STM0573 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8ZR49
#2: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A 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: 3.3 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 37.1000% 2-ethoxyethanol, 0.0500M calcium acetate, 0.1M Imidazole 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: 0.91837,0.97934,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 20, 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
10.918371
20.979341
30.979221
ReflectionResolution: 2.5→29.907 Å / Num. obs: 113412 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 48.836 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.563.80.811.63142282640.81100
2.56-2.643.80.6721.93081781110.672100
2.64-2.713.80.5882.33003678970.588100
2.71-2.83.80.492.72909676450.49100
2.8-2.893.80.3993.32820874060.399100
2.89-2.993.80.32742745272070.327100
2.99-3.13.80.2624.92644969540.262100
3.1-3.233.80.2056.22534666580.205100
3.23-3.373.80.15782447764270.157100
3.37-3.543.80.1349.82329861440.134100
3.54-3.733.80.10612.62224758820.106100
3.73-3.953.80.09314.72094355480.093100
3.95-4.233.80.07417.71972052390.074100
4.23-4.563.80.062211831748750.062100
4.56-53.80.05921.91700745350.059100
5-5.593.70.06120.41531340870.061100
5.59-6.453.70.06519.71355636490.065100
6.45-7.913.70.05723.21133230920.05799.9
7.91-11.183.60.04126.2879024530.04199.9
11.18-29.913.40.0426.7450613390.0494.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.907 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.422 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.222
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.2-ETHOXYETHANOL (ETX) AND IMIDAZOLE (IMD) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 5672 5 %RANDOM
Rwork0.203 ---
obs0.205 113329 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.18 Å2 / Biso mean: 27.788 Å2 / Biso min: 3.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--0.83 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14786 0 22 431 15239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02215161
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210108
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.96420619
X-RAY DIFFRACTIONr_angle_other_deg0.774324584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.45351931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.97423.544666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.066152474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.96915125
X-RAY DIFFRACTIONr_chiral_restr0.0680.22379
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02116990
X-RAY DIFFRACTIONr_gen_planes_other00.023105
X-RAY DIFFRACTIONr_mcbond_it0.63439586
X-RAY DIFFRACTIONr_mcbond_other0.16733907
X-RAY DIFFRACTIONr_mcangle_it1.339515355
X-RAY DIFFRACTIONr_scbond_it2.95685575
X-RAY DIFFRACTIONr_scangle_it4.254115255
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3917 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.310.5
BMEDIUM POSITIONAL0.320.5
CMEDIUM POSITIONAL0.370.5
DMEDIUM POSITIONAL0.250.5
EMEDIUM POSITIONAL0.410.5
FMEDIUM POSITIONAL0.440.5
AMEDIUM THERMAL0.332
BMEDIUM THERMAL0.332
CMEDIUM THERMAL0.342
DMEDIUM THERMAL0.312
EMEDIUM THERMAL0.342
FMEDIUM THERMAL0.372
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 420 -
Rwork0.322 7777 -
all-8197 -
obs--99.96 %
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)
11.70710.0339-0.12060.94210.27071.30410.0590.0862-0.21320.0862-0.02960.10480.0129-0.21-0.02940.0207-0.0088-0.01940.07610.01650.089736.134925.6419172.7951
21.6459-0.3395-0.05191.8261-0.00311.43870.0634-0.0560.02540.2016-0.0889-0.1069-0.1790.13250.02550.0699-0.0558-0.01510.05450.00360.01559.528939.0607182.9501
31.65430.2675-0.58121.0177-0.18631.38310.0098-0.0283-0.1337-0.0412-0.0287-0.0891-0.04940.14830.01890.01550.0101-0.01560.0434-0.0220.050891.666928.7837146.1315
41.1726-0.19470.07641.53870.40771.73110.06110.0590.0331-0.1025-0.01240.1344-0.2677-0.2411-0.04870.08780.07360.00910.1090.05950.061869.717544.128135.8868
51.9289-0.6501-0.3761.73830.33862.5303-0.0514-0.2547-0.18710.13090.14690.13230.09850.0347-0.09550.06520.0273-0.00450.07220.05120.05353.210273.4598108.2049
62.2990.74150.68851.55320.58451.7575-0.08-0.04640.2773-0.11210.0220.1489-0.3998-0.03420.0580.2019-0.00710.04940.03510.01430.082149.479895.215493.2573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 322
2X-RAY DIFFRACTION2B-5 - 321
3X-RAY DIFFRACTION3C-5 - 322
4X-RAY DIFFRACTION4D-5 - 322
5X-RAY DIFFRACTION5E-5 - 322
6X-RAY DIFFRACTION6F-3 - 322

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