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- PDB-3nre: Crystal structure of a Putative aldose 1-epimerase (b2544) from E... -

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Basic information

Entry
Database: PDB / ID: 3nre
TitleCrystal structure of a Putative aldose 1-epimerase (b2544) from ESCHERICHIA COLI K12 at 1.59 A resolution
ComponentsAldose 1-epimerase
KeywordsISOMERASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


aldose 1-epimerase activity / galactose catabolic process via UDP-galactose, Leloir pathway / glucose metabolic process / carbohydrate binding / DNA damage response
Similarity search - Function
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
DI(HYDROXYETHYL)ETHER / : / Uncharacterized protein YphB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.59 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative aldose 1-epimerase (b2544) from ESCHERICHIA COLI K12 at 1.59 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
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 / _struct_conn.pdbx_leaving_atom_flag
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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.5Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Aldose 1-epimerase
B: Aldose 1-epimerase
C: Aldose 1-epimerase
D: Aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,89023
Polymers131,9564
Non-polymers1,93419
Water19,7081094
1
A: Aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6267
Polymers32,9891
Non-polymers6376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4135
Polymers32,9891
Non-polymers4244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3074
Polymers32,9891
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5447
Polymers32,9891
Non-polymers5556
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.733, 72.005, 272.790
Angle α, β, γ (deg.)90.000, 90.700, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Aldose 1-epimerase


Mass: 32988.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: EcDH1_1124 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: C9QPM9, UniProt: P76584*PLUS
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1094 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.74 Å3/Da / Density % sol: 55.17 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M magnesium chloride, 20.0000% polyethylene glycol 8000, 0.1M TRIS pH 8.5, Additive 0.005M D-GLUCOSE, 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: 0.95369,0.97936,0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 10, 2010 / 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
10.953691
20.979361
30.97921
ReflectionResolution: 1.59→28.544 Å / Num. obs: 189340 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.942 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 10.54
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.59-1.650.2662.1567993726293.8
1.65-1.710.1932.9497443262894.8
1.71-1.790.1463.9564393695795.4
1.79-1.880.1045.4528283459495.8
1.88-20.0717.7566003708595.5
2-2.160.05310.4562633694994.7
2.16-2.370.04412.9520933422993.7
2.37-2.720.03616543653565492.3
2.72-3.420.02720.7523033406591
3.42-28.5440.02224.8520753339088.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.59→28.544 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.42 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.076
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.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.SOLVENT MOLECULES WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.PEG-200 AND PEG-8000 FRAGMENTS (PEG) AND MAGNESIUM (MG) FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 9534 5 %RANDOM
Rwork0.161 ---
obs0.162 189339 98.74 %-
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: 93.78 Å2 / Biso mean: 27.796 Å2 / Biso min: 11.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å2-0.2 Å2
2--0.84 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 1.59→28.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9204 0 127 1094 10425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02110262
X-RAY DIFFRACTIONr_bond_other_d0.0010.026970
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.93514129
X-RAY DIFFRACTIONr_angle_other_deg0.912316962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18551352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63923.709515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.662151486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6421560
X-RAY DIFFRACTIONr_chiral_restr0.1040.21450
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02111802
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022242
X-RAY DIFFRACTIONr_mcbond_it1.7436117
X-RAY DIFFRACTIONr_mcbond_other0.56932447
X-RAY DIFFRACTIONr_mcangle_it2.61559973
X-RAY DIFFRACTIONr_scbond_it3.86584145
X-RAY DIFFRACTIONr_scangle_it5.239114060
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 689 -
Rwork0.244 13184 -
all-13873 -
obs--98.29 %
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)
11.0224-0.30910.211.39970.98972.97550.11360.0006-0.04780.2205-0.1361-0.03740.464-0.13440.02250.1723-0.06280.00640.11120.00440.097518.78131.68655.9569
20.9289-0.1614-0.54480.9673-0.14143.1470.01060.11330.07020.04660.02520.0173-0.1891-0.5269-0.03580.03740.03880.00420.1724-0.00460.099617.740632.350412.1923
30.85440.5350.04711.4334-0.27581.6721-0.01590.0388-0.0635-0.02490.04080.03750.0454-0.0221-0.02490.02460.00980.00320.00780.00150.110816.5975-0.9528123.967
40.90010.3470.16330.91990.36592.1732-0.0820.11440.0605-0.09910.0346-0.0458-0.23920.1270.04730.0964-0.0529-0.02020.11630.02110.116217.6771-2.071280.2005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 290
2X-RAY DIFFRACTION2B0 - 290
3X-RAY DIFFRACTION3C0 - 290
4X-RAY DIFFRACTION4D0 - 290

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