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- PDB-3i7d: Crystal structure of sugar phosphate isomerase from a cupin super... -

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Basic information

Entry
Database: PDB / ID: 3i7d
TitleCrystal structure of sugar phosphate isomerase from a cupin superfamily SPO2919 from Silicibacter pomeroyi (YP_168127.1) from SILICIBACTER POMEROYI DSS-3 at 2.30 A resolution
Componentssugar phosphate isomerase
KeywordsISOMERASE / YP_168127.1 / sugar phosphate isomerase from a cupin superfamily SPO2919 from Silicibacter pomeroyi / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / sugar metabolism
Function / homology
Function and homology information


Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / DI(HYDROXYETHYL)ETHER / Cupin_2 domain-containing protein
Similarity search - Component
Biological speciesRuegeria pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of sugar phosphate isomerase from a cupin superfamily SPO2919 from Silicibacter pomeroyi (YP_168127.1) from SILICIBACTER POMEROYI DSS-3 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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: sugar phosphate isomerase
B: sugar phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4207
Polymers35,9452
Non-polymers4755
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-18 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.815, 52.815, 252.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A2 - 136
2112B2 - 136
1124A137 - 142
2124B137 - 142
1132A143 - 158
2132B143 - 158

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein sugar phosphate isomerase


Mass: 17972.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi DSS-3 (bacteria) / Gene: SPO2919, YP_168127.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LPC9

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Non-polymers , 5 types, 184 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.33
Details: 24.0000% polyethylene glycol 8000, 0.3000M sodium acetate, 0.1M sodium cacodylate pH 6.33, 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: 0.91837,0.97959,0.97941
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 18, 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
20.979591
30.979411
ReflectionResolution: 2.3→29.761 Å / Num. obs: 16869 / % possible obs: 99.9 % / Redundancy: 9.3 % / Biso Wilson estimate: 23.149 Å2 / Rmerge(I) obs: 0.336 / Rsym value: 0.336 / Net I/σ(I): 8.3
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.369.50.61123511881.20499.7
2.36-2.429.60.71131611821.09499.8
2.42-2.499.50.71091111471.03899.8
2.49-2.579.50.81060111130.97599.8
2.57-2.669.40.91026310950.825100
2.66-2.759.511000510520.731100
2.75-2.859.41.3944010020.609100
2.85-2.979.41.5943610040.49799.9
2.97-3.19.41.889909550.416100
3.1-3.259.42.283608920.34199.9
3.25-3.439.3380648710.25599.9
3.43-3.649.33.976298190.19599.9
3.64-3.899.24.173097940.18499.9
3.89-4.29.25.367447340.14100
4.2-4.69.16.461706790.11699.9
4.6-5.148.96.456836350.115100
5.14-5.948.74.850235770.155100
5.94-7.278.64.441434830.169100
7.27-10.298.1632994050.125100
10.29-29.766.98.916722420.0895.3

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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: 2.3→29.761 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 7.302 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.23
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. CHLORIDE (CL), CACODYLATE (CAC) AND ACETATE (ACT) IONS, AND PEG8000 FRAGMENT(PEG) MOLECULES ARE MODELED BASED ON CRYSTALLIZATION CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 850 5.1 %RANDOM
Rwork0.196 ---
obs0.198 16826 99.75 %-
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: 90.7 Å2 / Biso mean: 32.484 Å2 / Biso min: 13.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 22 179 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222443
X-RAY DIFFRACTIONr_bond_other_d0.0020.021658
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9743303
X-RAY DIFFRACTIONr_angle_other_deg0.88634023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.21523.86114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24815385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1461520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022780
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02492
X-RAY DIFFRACTIONr_nbd_refined0.1950.2449
X-RAY DIFFRACTIONr_nbd_other0.2010.21755
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21146
X-RAY DIFFRACTIONr_nbtor_other0.0850.21377
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2160
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.26
X-RAY DIFFRACTIONr_mcbond_it1.64431839
X-RAY DIFFRACTIONr_mcbond_other0.3573645
X-RAY DIFFRACTIONr_mcangle_it2.08142493
X-RAY DIFFRACTIONr_scbond_it3.15959
X-RAY DIFFRACTIONr_scangle_it4.0016810
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1787TIGHT POSITIONAL0.060.05
1948MEDIUM POSITIONAL0.280.5
1787TIGHT THERMAL0.180.5
1948MEDIUM THERMAL0.922
271MEDIUM POSITIONAL0.670.5
271MEDIUM THERMAL1.322
393TIGHT POSITIONAL0.050.05
3107MEDIUM POSITIONAL0.120.5
393TIGHT THERMAL0.130.5
3107MEDIUM THERMAL0.532
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 68 -
Rwork0.256 1120 -
all-1188 -
obs--99.5 %

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