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- PDB-5vhu: E. coli CFT073 c3406 -

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Basic information

Entry
Database: PDB / ID: 5vhu
TitleE. coli CFT073 c3406
ComponentsIsomerase
KeywordsISOMERASE / Sugar isomerase domain / arabinose-5-phosphate isomerase / API
Function / homologyGlucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCech, D.L. / Pratt, A.C. / Woodard, R.W.
CitationJournal: To Be Published
Title: Insights into the mechanism of arabinose-5-phosphate isomerases.
Authors: Cech, D.L. / Pratt, A.C. / Cheng, M. / Barraza, S. / Yep, A. / Holler, T.P. / Woodard, R.W.
History
DepositionApr 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0082
Polymers20,9121
Non-polymers961
Water1,53185
1
A: Isomerase
hetero molecules

A: Isomerase
hetero molecules

A: Isomerase
hetero molecules

A: Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0338
Polymers83,6494
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area17030 Å2
ΔGint-209 kcal/mol
Surface area25530 Å2
MethodPISA
2
A: Isomerase
hetero molecules

A: Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0164
Polymers41,8242
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area5510 Å2
ΔGint-83 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.832, 71.489, 77.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Isomerase


Mass: 20912.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: OK10_20845 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A148HHT8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.37 Å3/Da / Density % sol: 48.12 % / Description: colorless rods
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic pH 5.6, 0.5 M NaCl, 2% v/v ethylene imine polymer

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→52.6 Å / Num. obs: 17785 / % possible obs: 99.85 % / Redundancy: 14.7 % / Rsym value: 0.072 / Net I/σ(I): 10.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FXA

3fxa


Resolution: 1.8→52.6 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.949 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.20806 961 5.1 %RANDOM
Rwork0.17353 ---
obs0.17523 17785 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.962 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---0.6 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.8→52.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 5 85 1495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191433
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.9721942
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5355187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4212550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20815249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.608153
X-RAY DIFFRACTIONr_chiral_restr0.1370.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211026
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1761.275751
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6931.901937
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4551.612681
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.29118.3232092
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 66 -
Rwork0.188 1300 -
obs--99.35 %

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