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- PDB-4q0v: Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase mu... -

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Basic information

Entry
Database: PDB / ID: 4q0v
TitleCrystal structure of Acinetobacter sp. DL28 L-ribose isomerase mutant E204Q in complex with L-ribulose
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
: / COBALT HEXAMMINE(III) / L-ribulose / alpha-L-ribulofuranose / L-Ribose isomerase
Similarity search - Component
Biological speciesAcinetobacter (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 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 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.type / _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 1.3Aug 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 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Aug 12, 2026Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.formula / _pdbx_struct_conn_angle.ptnr1_label_atom_id ..._chem_comp.formula / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_label_atom_id
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-Ribose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,02110
Polymers28,7501
Non-polymers1,2719
Water1,820101
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)120,08540
Polymers115,0014
Non-polymers5,08436
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 area14450 Å2
ΔGint-66 kcal/mol
Surface area35020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.850, 107.350, 118.180
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: 28750.270 Da / Num. of mol.: 1 / Mutation: E204Q
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, 7 molecules

#3: Sugar ChemComp-QDK / L-ribulose


Type: L-saccharide / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
#4: Sugar
ChemComp-RUU / alpha-L-ribulofuranose / alpha-L-ribulose / L-ribulose / ribulose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LRulfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-ribulofuranoseCOMMON NAMEGMML 1.0
a-L-RulfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 103 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


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.47 %
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: Apr 12, 2012 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→21.8 Å / Num. all: 21360 / Num. obs: 21360 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.6
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2121 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.3refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4Q0P

4q0p


Resolution: 1.98→21.77 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2781687.42 / 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
Rfree0.243 2122 9.9 %RANDOM
Rwork0.203 ---
all0.207 21360 --
obs0.203 21360 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.3035 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1--4.26 Å20 Å20 Å2
2---4.77 Å20 Å2
3---9.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.98→21.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 78 101 2109
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_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 1.98→2.05 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.324 205 9.7 %
Rwork0.301 1916 -
obs-1916 99.9 %
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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