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- PDB-3q1n: Crystal structure of a galactose mutarotase-like protein (LSEI_25... -

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Basic information

Entry
Database: PDB / ID: 3q1n
TitleCrystal structure of a galactose mutarotase-like protein (LSEI_2598) from Lactobacillus casei ATCC 334 at 1.61 A resolution
ComponentsGalactose mutarotase related enzyme
KeywordsISOMERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


isomerase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Protein LacX / Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
NITRATE ION / Galactose mutarotase related enzyme
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.61 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a galactose mutarotase-like protein (LSEI_2598) from Lactobacillus casei ATCC 334 at 1.61 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 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 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galactose mutarotase related enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,81720
Polymers32,6921
Non-polymers1,12619
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.152, 67.076, 93.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsANALYSTICAL SIZE EXCLUSION CHROMATOGRAPHY INDICATES THAT A MONOMER IS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Galactose mutarotase related enzyme


Mass: 32691.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Strain: ATCC 334 / Gene: LSEI_2598 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q034Q3
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 277 K / pH: 6.3
Details: 0.20M NH4NO3, 20.00% PEG-3350, No Buffer pH 6.3, 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: 0.91837,0.97903,0.97881
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 24, 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
20.979031
30.978811
ReflectionResolution: 1.61→36.529 Å / Num. obs: 40969 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.582 % / Biso Wilson estimate: 16.25 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.86
Reflection shellResolution: 1.61→1.67 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0109refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.61→36.53 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.174 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.081
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. NITRATE (NO3) FROM THE CRYSTALLIZATION: CHLORIDE (CL) FROM THE PURIFICATION BUFFER; AND ETHYLENE GLYCOL(EDO), USED AS A CRYOPROTECTANT, WERE MODELED INTO THE STRUCTURE. 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5.SOLVENT RESIDUES WERE EXCLUDED FROM TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2056 5 %RANDOM
Rwork0.155 ---
obs0.157 40912 99.8 %-
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 mean: 21.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2---0.46 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.61→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 70 333 2702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222627
X-RAY DIFFRACTIONr_bond_other_d0.0010.021799
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9683593
X-RAY DIFFRACTIONr_angle_other_deg0.85334439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53524.836122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.815433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.165159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02520
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6551.51586
X-RAY DIFFRACTIONr_mcbond_other0.1821.5626
X-RAY DIFFRACTIONr_mcangle_it1.1322578
X-RAY DIFFRACTIONr_scbond_it1.88231041
X-RAY DIFFRACTIONr_scangle_it2.9774.5982
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 165 -
Rwork0.246 2825 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: 9.3263 Å / Origin y: 30.226 Å / Origin z: 14.628 Å
111213212223313233
T0.0436 Å20.0002 Å20.0016 Å2-0.0507 Å2-0.0005 Å2--0.0499 Å2
L0.2891 °2-0.1097 °20.0599 °2-0.5381 °20.105 °2--0.2954 °2
S0.01 Å °-0.0107 Å °0.0242 Å °-0.0194 Å °-0.0254 Å °0.0506 Å °-0.0225 Å °-0.0629 Å °0.0155 Å °

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