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- PDB-4q0p: Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase in... -

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Basic information

Entry
Database: PDB / ID: 4q0p
TitleCrystal structure of Acinetobacter sp. DL28 L-ribose isomerase in complex with L-ribose
ComponentsL-Ribose isomerase
KeywordsISOMERASE / Cupin barrel / Sugar binding
Function / homology
Function and homology information


RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-L-ribopyranose / : / COBALT HEXAMMINE(III) / alpha-L-ribofuranose / L-Ribose isomerase
Similarity search - Component
Biological speciesAcinetobacter (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsYoshida, H. / Yoshihara, A. / Teraoka, M. / Izumori, K. / Kamitori, S.
Citation
Journal: Febs J. / Year: 2014
Title: X-ray structure of a novel L-ribose isomerase acting on a non-natural sugar L-ribose as its ideal substrate.
Authors: Yoshida, H. / Yoshihara, A. / Teraoka, M. / Terami, Y. / Takata, G. / Izumori, K. / Kamitori, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Overexpression, crystallization and preliminary X-ray diffraction analysis of L-ribose isomerase from Acinetobacter sp. strain DL-28
Authors: Yoshida, H. / Teraoka, M. / Yoshihara, A. / Izumori, K. / Kamitori, S.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Apr 3, 2024Group: 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: L-Ribose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5727
Polymers28,7511
Non-polymers8216
Water2,576143
1
A: L-Ribose isomerase
hetero molecules

A: L-Ribose isomerase
hetero molecules

A: L-Ribose isomerase
hetero molecules

A: L-Ribose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,28728
Polymers115,0054
Non-polymers3,28224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area14740 Å2
ΔGint-55 kcal/mol
Surface area35930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.380, 107.930, 119.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein L-Ribose isomerase


Mass: 28751.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter (bacteria) / Strain: DL-28 / Gene: L-RI / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q93UQ5, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds

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Sugars , 2 types, 4 molecules

#3: Sugar ChemComp-0MK / beta-L-ribopyranose / beta-L-ribose / L-ribose / ribose / L-ribopyranose / Ribose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-ribopyranoseCOMMON NAMEGMML 1.0
b-L-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-Z6J / alpha-L-ribofuranose / alpha-L-ribose / L-ribose / ribose / Ribose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-ribofuranoseCOMMON NAMEGMML 1.0
a-L-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 145 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-16%(v/v) PEG400, 0.2M NaCl, 0.1M HEPES, 0.02M Hexaammine cobalt(III) chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 8, 2011 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→20.5 Å / Num. all: 23208 / Num. obs: 23208 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.1
Reflection shellResolution: 1.93→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2294 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.3refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The structure model of selenomethione derivative solved by MAD

Resolution: 1.93→20.49 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 6974531.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2288 9.9 %RANDOM
Rwork0.208 ---
all0.211 23208 --
obs0.208 23208 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.9429 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.98 Å20 Å20 Å2
2---4.67 Å20 Å2
3---9.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 1.93→20.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 48 143 2121
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 1.93→2 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.365 230 10 %
Rwork0.33 2067 -
obs-2067 99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6ligand.paramligand.top

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