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- PDB-2g0w: CRYSTAL STRUCTURE OF A PUTATIVE SUGAR ISOMERASE (LMO2234) FROM LI... -

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Basic information

Entry
Database: PDB / ID: 2g0w
TitleCRYSTAL STRUCTURE OF A PUTATIVE SUGAR ISOMERASE (LMO2234) FROM LISTERIA MONOCYTOGENES AT 1.70 A RESOLUTION
ComponentsLmo2234 protein
KeywordsHYDROLASE / PUTATIVE SUGAR ISOMERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyDivalent-metal-dependent TIM barrel enzymes / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / :
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Lmo2234 protein (16411704) from Listeria monocytogenes LI2 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.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: Lmo2234 protein
B: Lmo2234 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1957
Polymers66,9032
Non-polymers2915
Water8,719484
1
A: Lmo2234 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5254
Polymers33,4521
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lmo2234 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6703
Polymers33,4521
Non-polymers2192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.832, 61.249, 70.428
Angle α, β, γ (deg.)90.00, 91.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lmo2234 protein


Mass: 33451.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: Li2 / Gene: 16411704 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4EPT5
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O

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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: 1.99 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8
Details: 25.0% PEG-3350, 0.2M MAGNESIUM ACETATE, 0.1M TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999, 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99991
20.97971
ReflectionResolution: 1.7→28.894 Å / Num. obs: 58181 / % possible obs: 98.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRsym value% possible all
1.7-1.742.50.8270.9960837930.82788.4
1.74-1.792.80.6561.11140240460.65696.1
1.79-1.843.50.5661.31401940520.56699.9
1.84-1.93.60.4511.71453840270.45199.9
1.9-1.963.60.3252.31400038840.32599.9
1.96-2.033.60.25531356137380.255100
2.03-2.113.60.2013.71310136200.201100
2.11-2.193.60.1614.71255434650.161100
2.19-2.293.60.1395.31208433420.139100
2.29-2.43.60.1176.31152631920.117100
2.4-2.533.60.10471103830600.104100
2.53-2.693.60.098.11035128740.09100
2.69-2.873.60.0779.3970727120.077100
2.87-3.13.60.0699.9909225410.069100
3.1-3.43.50.05511.9825323270.05599.8
3.4-3.83.50.04812.9737421100.04899.5
3.8-4.393.40.04414633518800.044100
4.39-5.383.30.0414.7518315760.04100
5.38-7.63.70.0320.9458112470.03100
7.6-28.893.50.02523.224286950.02598.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→28.89 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.824 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.123
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. RESIDUES 1-9 IN CHAIN A AND 284 IN CHAIN B WERE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. 2 HIS RESIDUES OF THE HIS-TAG ARE ORDERED IN CHAIN B.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2940 5.1 %RANDOM
Rwork0.189 ---
obs0.191 58148 98.64 %-
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 mean: 16.592 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å2-0.75 Å2
2---0.49 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4345 0 17 484 4846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224476
X-RAY DIFFRACTIONr_bond_other_d0.0010.024073
X-RAY DIFFRACTIONr_angle_refined_deg1.641.9556055
X-RAY DIFFRACTIONr_angle_other_deg0.88439482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32824.757206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56215775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.941527
X-RAY DIFFRACTIONr_chiral_restr0.0920.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
X-RAY DIFFRACTIONr_nbd_refined0.2160.21040
X-RAY DIFFRACTIONr_nbd_other0.1850.24340
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22206
X-RAY DIFFRACTIONr_nbtor_other0.0890.22469
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2429
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0610.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.240
X-RAY DIFFRACTIONr_mcbond_it1.65723055
X-RAY DIFFRACTIONr_mcbond_other0.33321144
X-RAY DIFFRACTIONr_mcangle_it2.33744489
X-RAY DIFFRACTIONr_scbond_it4.32361866
X-RAY DIFFRACTIONr_scangle_it5.52481565
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 189 -
Rwork0.281 3592 -
obs-3781 87.14 %

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