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- PDB-4hgx: Crystal structure of xylose isomerase domain containing protein (... -

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Basic information

Entry
Database: PDB / ID: 4hgx
TitleCrystal structure of xylose isomerase domain containing protein (stm4435) from salmonella typhimurium lt2 with unknown ligand
ComponentsXylose isomerase domain containing protein
KeywordsISOMERASE / xylose isomerase domain / unknown ligand
Function / homology
Function and homology information


racemase and epimerase activity, acting on carbohydrates and derivatives / manganese ion binding
Similarity search - Function
Uncharacterised conserved protein UCP036778, sugar epimerase-type / 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
ACETATE ION / Cytoplasmic protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsBoyko, K.M. / Gorbacheva, M.A. / Korzhenevskiy, D.A. / Dorovatovsky, P.V. / Rakitina, T.V. / Lipkin, A.V. / Shumilin, I.A. / Minor, W. / Popov, V.O.
CitationJournal: To be Published
Title: Crystal structure of xylose isomerase domain containing protein (stm4435) from salmonella typhimurium lt2 with unknown ligand
Authors: Boyko, K.M. / Gorbacheva, M.A. / Korzhenevskiy, D.A. / Dorovatovsky, P.V. / Rakitina, T.V. / Lipkin, A.V. / Shumilin, I.A. / Minor, W. / Popov, V.O.
History
DepositionOct 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylose isomerase domain containing protein
B: Xylose isomerase domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8716
Polymers61,6222
Non-polymers2494
Water1,892105
1
A: Xylose isomerase domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9363
Polymers30,8111
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xylose isomerase domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9363
Polymers30,8111
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.180, 93.180, 125.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Xylose isomerase domain containing protein


Mass: 30811.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: lt2 / Gene: STM4435 / Plasmid: pET-24 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q8ZK48
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.01M Cobalt(II) chloride hexahydrate, 0.1M MES monohydrate pH 6.5, 1.8M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.985 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 21, 2011 / Details: NON
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.985 Å / Relative weight: 1
ReflectionResolution: 2.6→29.46 Å / Num. all: 17564 / Num. obs: 17523 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.35 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 17.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.6-2.960.6314.9768747549799.3
2.96-3.160.3678.9526489208999.9
3.16-3.40.25112.9524548191599.9
3.4-3.70.16618.822469174999.9
3.7-4.20.11125.28247511936100
4.2-4.80.07534.3717708139599.9
4.8-60.08330.1417615140899.9
6-80.07133.451078287499.3
8-300.03162.22772666095
30

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
AUTOMARdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q02

2q02


Resolution: 2.6→29.15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.855 / WRfactor Rfree: 0.2491 / WRfactor Rwork: 0.1558 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7674 / SU B: 14.299 / SU ML: 0.304 / SU Rfree: 0.4071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3024 883 5.1 %RANDOM
Rwork0.1907 ---
obs0.1962 17477 99.44 %-
all-22226 --
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 max: 118.77 Å2 / Biso mean: 36.9779 Å2 / Biso min: 10.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4167 0 10 105 4282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194253
X-RAY DIFFRACTIONr_angle_refined_deg2.2761.9635762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2385537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.59424.15200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.03715703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4531533
X-RAY DIFFRACTIONr_chiral_restr0.1350.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213245
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 67 -
Rwork0.261 1028 -
all-1095 -
obs--96.82 %

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