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- PDB-3fxa: Crystal structure of a putative sugar-phosphate isomerase (lmof23... -

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Basic information

Entry
Database: PDB / ID: 3fxa
TitleCrystal structure of a putative sugar-phosphate isomerase (lmof2365_0531) from listeria monocytogenes str. 4b f2365 at 1.60 A resolution
ComponentsSIS domain protein
KeywordsSUGAR BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyGlucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesListeria monocytogenes str. 4b F2365 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / MAD, molecular replacement / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative sugar-phosphate isomerase (YP_013136.1) from Listeria monocytogenes 4b F2365 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 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 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIS domain protein
B: SIS domain protein
C: SIS domain protein
D: SIS domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6376
Polymers86,5134
Non-polymers1242
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16170 Å2
ΔGint-159.6 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.944, 57.944, 197.964
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
AA
BB
CC
DD

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A2 - 186
2116B2 - 186
3116C2 - 186
4116D2 - 186

NCS ensembles :
ID
1
A
B
C
D
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
SIS domain protein


Mass: 21628.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes str. 4b F2365 (bacteria)
Strain: F2365, serotype 4b / Gene: LMOf2365_0531, YP_013136.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q723E8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.2244.54DATA FROM A SE-MET CONTAINING CRYSTAL IN SPACEGROUP P2(1) WAS USED FOR THE MAD PHASING EXPERIMENTS AT 1.75 ANGSTROMS RESOLUTION. ONE OF THE TETRAMERS FROM THIS AUTOTRACED MAD STRUCTURE WAS USED AS A MOLECULAR REPLACEMENT SEARCH MODEL TO PHASE THIS STRUCTURE AT 1.6 ANGSTROMS RESOLUTION IN THE P3(1) SPACEGROUP. MODEL COMPLETION AND REFINEMENT WERE AGAINST THE P3(1) DATA.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop5.9NANODROP, 0.2M Mg formate, 20.0% PEG 3350, No Buffer pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop6.3NANODROP, 0.2M NH4Cl, 20.0% PEG 3350, No Buffer pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.94645
SYNCHROTRONAPS 23-ID-B20.97966, 0.94645
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDOct 11, 2008Adjustable focusing mirrors in K-B geometry
MARMOSAIC 300 mm CCD2CCDOct 12, 2008Adjustable focusing mirrors in K-B geometry
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) Double crystalMADMx-ray1
2Si(111) Double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979661
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11h,k,l10.561
11-k,-h,-l20.439
ReflectionResolution: 1.6→28.976 Å / Num. obs: 97660 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 20.164 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 5.726
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.643.30.6521.82312770530.65297.2
1.64-1.693.80.5862.32643070100.58699.3
1.69-1.743.80.4592.82586568470.45999.4
1.74-1.793.80.3643.52522966570.36499.6
1.79-1.853.80.284.52447564320.2899.6
1.85-1.913.80.2165.72392862730.21699.7
1.91-1.983.80.1667.42290159930.16699.8
1.98-2.073.80.1369.42244258420.13699.8
2.07-2.163.80.11511.82123855570.11599.8
2.16-2.263.80.1142019952700.199.9
2.26-2.393.90.08515.51975551210.085100
2.39-2.533.90.07217.71850947950.072100
2.53-2.76.40.14320.62877944620.143100
2.7-2.927.30.13123.43061342070.131100
2.92-3.27.40.10127.22870338740.101100
3.2-3.587.50.07832.22629035060.078100
3.58-4.137.50.06436.72298830690.064100
4.13-5.067.60.05339.91953225730.053100
5.06-7.167.60.05638.81553920350.056100
7.16-28.9767.50.05141818310840.05198.8

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Phasing

PhasingMethod: MAD, molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLM7.0.1data reduction
SCALA3.2.5data scaling
SHELXphasing
SHARP2.2.0phasing
PHASER1.3.3phasing
REFMAC5.5.0053refinement
MolProbity3beta29model building
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.6→28.976 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 1.558 / SU ML: 0.025 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ETHYLENE GLYCOL MOLECULES FROM THE CRYO SOLUTION ARE MODELED. 5. THE DIFFRACTION DATA IS TWINNED WITH OPERATOR "-K, -H, -L". THE TWINNING FRACTION IS REFINED TO 0.4387. 6. REFLECTIONS FOR FREE-R SET WERE SELECTED ON RANDOM + TWIN LAW BASIS. 7. THERE IS SOME UNMODELED DENSITY NEAR RESIDUE D188.
RfactorNum. reflection% reflectionSelection details
Rfree0.157 4850 5 %RANDOM + TWIN LAW
Rwork0.133 ---
obs0.135 97613 99.5 %-
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: 54.34 Å2 / Biso mean: 18.562 Å2 / Biso min: 5.87 Å2
Baniso -1Baniso -2Baniso -3
1-4.62 Å20 Å20 Å2
2--4.62 Å20 Å2
3----9.24 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5695 0 8 443 6146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225984
X-RAY DIFFRACTIONr_bond_other_d0.0030.023904
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.978169
X-RAY DIFFRACTIONr_angle_other_deg1.33939759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4735819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65126.376218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.881151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8581510
X-RAY DIFFRACTIONr_chiral_restr0.0940.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216635
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021031
X-RAY DIFFRACTIONr_mcbond_it1.15423896
X-RAY DIFFRACTIONr_mcbond_other0.26721574
X-RAY DIFFRACTIONr_mcangle_it1.82246364
X-RAY DIFFRACTIONr_scbond_it3.22962088
X-RAY DIFFRACTIONr_scangle_it4.57481776
Refine LS restraints NCS

Number: 2066 / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDTypeRms dev position (Å)Weight position
AAALOOSE POSITIONAL0.195
BBBLOOSE POSITIONAL0.365
CCCLOOSE POSITIONAL0.225
DDDLOOSE POSITIONAL0.195
AAALOOSE THERMAL1.4610
BBBLOOSE THERMAL1.7310
CCCLOOSE THERMAL1.5110
DDDLOOSE THERMAL1.4910
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 349 -
Rwork0.195 6588 -
all-6937 -
obs--96.39 %
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)
10.3762-0.04840.0090.10290.05780.6029-0.0212-0.00880.02680.00990.0058-0.0052-0.0446-0.05850.01550.0231-0.0191-0.00320.0574-0.0020.0024-14.212.333-3.015
20.3897-0.1475-0.24110.07450.01480.5769-0.0262-0.0637-0.00680.0120.00960.0015-0.00640.07130.01650.0281-0.0238-0.00450.06220.00480.00144.49710.51-0.459
30.17010.0647-0.10160.35220.08220.46980.00840.01540.0116-0.0455-0.01840.0168-0.0349-0.01420.01010.0338-0.0205-0.00140.0440.00170.00182.41714.958-31.566
40.16720.1404-0.21210.2299-0.07080.5195-0.03170.0117-0.0231-0.0222-0.0173-0.00490.0696-0.03270.0490.0421-0.03230.00520.0463-0.00540.0055-5.666-2.216-29.405
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 192
2X-RAY DIFFRACTION2B0 - 190
3X-RAY DIFFRACTION3C0 - 190
4X-RAY DIFFRACTION4D1 - 190

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