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- PDB-3i0z: Crystal structure of putative putative tagatose-6-phosphate ketos... -

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Entry
Database: PDB / ID: 3i0z
TitleCrystal structure of putative putative tagatose-6-phosphate ketose/aldose isomerase (NP_344614.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 1.70 A resolution
Componentsputative tagatose-6-phosphate ketose/aldose isomerase
KeywordsISOMERASE / NP_344614.1 / putative putative tagatose-6-phosphate ketose/aldose isomerase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding / isomerase activity / hydrolase activity
Similarity search - Function
AgaS, SIS domain / 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
PHOSPHATE ION / Sugar isomerase domain protein AgaS / Sugar isomerase domain protein AgaS
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (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 putative tagatose-6-phosphate ketose/aldose isomerase (NP_344614.1) from STREPTOCOCCUS PNEUMONIAE TIGR4 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: 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 tagatose-6-phosphate ketose/aldose isomerase
B: putative tagatose-6-phosphate ketose/aldose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,97719
Polymers86,8832
Non-polymers1,09417
Water14,862825
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-6 kcal/mol
Surface area25410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.635, 111.267, 126.600
Angle α, β, γ (deg.)90.000, 97.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein putative tagatose-6-phosphate ketose/aldose isomerase / Sugar isomerase domain protein AgaS


Mass: 43441.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Gene: agaS, NP_344614.1, SP_0065 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97T85, UniProt: A0A0H2UN25*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / 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.

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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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1860M calcium acetate, 22.2000% polyethylene glycol 3350, 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: 0.91837,0.97964
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 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
20.979641
ReflectionResolution: 1.7→29.748 Å / Num. obs: 85864 / % possible obs: 99 % / Redundancy: 2.8 % / Biso Wilson estimate: 16.104 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 7.225
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.742.80.5321.41757363030.53298
1.74-1.792.80.4281.71709661120.42898.4
1.79-1.842.80.3442.11667059630.34498.5
1.84-1.92.80.2782.61628758130.27898.4
1.9-1.962.80.2263.21570155950.22698.5
1.96-2.032.80.1923.81535454730.19298.7
2.03-2.112.80.154.81474952520.1598.8
2.11-2.192.80.1255.81428950920.12599
2.19-2.292.80.1096.51372248810.10999
2.29-2.42.80.0957.31313046720.09599
2.4-2.532.80.0897.81249744430.08999.5
2.53-2.692.80.0828.21180842080.08299.5
2.69-2.872.80.0689.61123040050.06899.5
2.87-3.12.80.0610.91036836810.0699.7
3.1-3.42.80.0512.3956334090.0599.7
3.4-3.82.80.04314.4868130930.04399.9
3.8-4.392.80.04214.1768827410.04299.9
4.39-5.382.80.04513651723270.045100
5.38-7.62.80.04713.4500918090.047100
7.6-29.752.70.03913.726879920.03998.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.748 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 3.642 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.091
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 ANION AND ETHYLENE GLYCOL MOLECULES FROM CRYSTALLIZATION
RfactorNum. reflection% reflectionSelection details
Rfree0.178 4302 5 %RANDOM
Rwork0.139 ---
obs0.141 85861 98.87 %-
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: 68.36 Å2 / Biso mean: 20.225 Å2 / Biso min: 7.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20.13 Å2
2--0.46 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6021 0 67 825 6913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226401
X-RAY DIFFRACTIONr_bond_other_d0.0010.024191
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9698717
X-RAY DIFFRACTIONr_angle_other_deg0.863310271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41124.513277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.772151048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5411532
X-RAY DIFFRACTIONr_chiral_restr0.0970.21021
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027218
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021294
X-RAY DIFFRACTIONr_nbd_refined0.2220.31410
X-RAY DIFFRACTIONr_nbd_other0.20.34537
X-RAY DIFFRACTIONr_nbtor_refined0.1870.53237
X-RAY DIFFRACTIONr_nbtor_other0.0910.53158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.51232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4420.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4220.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2920.561
X-RAY DIFFRACTIONr_mcbond_it1.98234294
X-RAY DIFFRACTIONr_mcbond_other0.57231622
X-RAY DIFFRACTIONr_mcangle_it2.49656511
X-RAY DIFFRACTIONr_scbond_it4.37382606
X-RAY DIFFRACTIONr_scangle_it5.585112206
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 348 -
Rwork0.196 5952 -
all-6300 -
obs--97.89 %
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)
10.7770.08120.08910.3270.07670.44730.0366-0.1566-0.01790.0722-0.01960.0558-0.0048-0.0403-0.017-0.0244-0.01190.0118-0.02730.006-0.04157.817464.851343.8185
20.72760.03790.08590.3680.09390.45610.00630.13540.0087-0.0580.0084-0.0122-0.0690.0476-0.0147-0.0269-0.01210.0059-0.02720.0008-0.054917.504669.590717.944
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 387
2X-RAY DIFFRACTION2B0 - 387

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