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- PDB-3qc0: Crystal structure of a sugar isomerase (SMc04130) from SINORHIZOB... -

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Basic information

Entry
Database: PDB / ID: 3qc0
TitleCrystal structure of a sugar isomerase (SMc04130) from SINORHIZOBIUM MELILOTI 1021 at 1.45 A resolution
Componentssugar isomerase
KeywordsISOMERASE / TIM BARREL / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


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
Similarity search - Domain/homology
Unknown ligand / Xylose isomerase-like TIM barrel domain-containing protein
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a sugar isomerase (SMc04130) from SINORHIZOBIUM MELILOTI 1021 at 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,73613
Polymers29,7281
Non-polymers2,00812
Water4,810267
1
A: sugar isomerase
hetero molecules

A: sugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,47226
Polymers59,4562
Non-polymers4,01524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area9000 Å2
ΔGint-21 kcal/mol
Surface area20470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.796, 70.796, 264.721
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein sugar isomerase


Mass: 29728.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R00122, SMc04130 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q92T58
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 3.22 Å3/Da / Density % sol: 61.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50.0% PEG-200, 0.1M HEPES 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: 0.91837,0.97929,0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 12, 2010 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979291
30.979151
ReflectionResolution: 1.45→29.865 Å / Num. all: 70842 / Num. obs: 70842 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 16.06 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.45-1.495.80.6922.32980351090.69299.8
1.49-1.535.90.5331.42925350000.53399.9
1.53-1.575.90.4341.82857548820.43499.9
1.57-1.625.90.3582.22759447080.358100
1.62-1.675.90.2952.62686745760.295100
1.67-1.735.90.2493.12622544610.249100
1.73-1.85.90.1963.92523543050.196100
1.8-1.875.90.1534.92437141560.153100
1.87-1.965.90.1275.72348039990.127100
1.96-2.055.80.1066.52232938180.106100
2.05-2.165.90.09472153736760.094100
2.16-2.295.80.08972023334680.089100
2.29-2.455.80.0867.31910832790.086100
2.45-2.655.80.0738.41773130510.073100
2.65-2.95.80.0639.41647028420.063100
2.9-3.245.70.05411.21496926140.054100
3.24-3.745.70.04712.11316323170.047100
3.74-4.595.50.047121102719890.047100
4.59-6.485.40.04712867416170.047100
6.48-29.8654.70.04512.145929750.04598.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→29.865 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.19 / SU B: 2.285 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.053
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS 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. THE IDENTITY OF THE METAL SITE WAS TENTATIVELY ASSIGNED AS A PARTIAL OCCUPANCY ZINC SITE BASED ON THE PRESENCE OF ZINC IN A X-RAY FLUORESCENCE EXCITATION SCAN. HOWEVER, OTHER METALS WERE ALSO PRESENT IN THE SCAN WITH LOWER PEAK HEIGHTS. THE CHANGE IN ANOMALOUS DIFFERENCE DENSITY PEAK HEIGHTS CALCULATED WITH DATA COLLECTED ABOVE AND BELOW THE ZINC K-ABSORPTION EDGE SHOWS ONLY A SMALL DECREASE SUGGESTING THAT ADDITIONAL METALS MAY BE BOUND AT THE SITE. HOMOLOGOUS STRUCTURES HAVE BOTH ZN (PDB ID: 1I6N, 2Q02, 3JU2) AND MN (PDB ID: 2OU4, 2QUL, 2QUM, 2QUN) IONS MODELED AT THIS SITE. 7. TETRAETHYLENE GLYCOL (PG4) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 8. AN UNKNOWN LIGAND (UNL) IS MODELED NEAR ZINC ION. 9. ATOM OCCUPANCIES WERE REFINED WITH PHENIX.REFINE SOFTWARE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1846 3571 5 %RANDOM
Rwork0.1594 ---
obs0.1607 70726 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 68.64 Å2 / Biso mean: 24.3082 Å2 / Biso min: 10.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å21.04 Å20 Å2
2--2.09 Å20 Å2
3----3.13 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 101 267 2409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222271
X-RAY DIFFRACTIONr_bond_other_d0.0010.021588
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.9893071
X-RAY DIFFRACTIONr_angle_other_deg0.95233872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14323.08594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88615354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5811522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212552
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02448
X-RAY DIFFRACTIONr_mcbond_it1.5381.51415
X-RAY DIFFRACTIONr_mcbond_other0.9811.5586
X-RAY DIFFRACTIONr_mcangle_it2.22322264
X-RAY DIFFRACTIONr_scbond_it3.1893856
X-RAY DIFFRACTIONr_scangle_it4.7014.5798
X-RAY DIFFRACTIONr_rigid_bond_restr1.6833852
X-RAY DIFFRACTIONr_sphericity_free10.7283276
X-RAY DIFFRACTIONr_sphericity_bonded6.33633809
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 243 -
Rwork0.248 4852 -
all-5095 -
obs--99.63 %
Refinement TLS params.Method: refined / Origin x: -12.502 Å / Origin y: 44.422 Å / Origin z: 0.704 Å
111213212223313233
T0.0532 Å2-0.0184 Å2-0.0171 Å2-0.0207 Å20.0075 Å2--0.0513 Å2
L0.0117 °2-0.0383 °20.0878 °2-0.5721 °2-0.6483 °2--0.8998 °2
S0.0118 Å °-0.0284 Å °-0.0039 Å °-0.1413 Å °0.0495 Å °0.0127 Å °0.1699 Å °-0.0735 Å °-0.0614 Å °

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