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- PDB-3ww1: X-ray structure of Cellulomonas parahominis L-ribose isomerase wi... -

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Basic information

Entry
Database: PDB / ID: 3ww1
TitleX-ray structure of Cellulomonas parahominis L-ribose isomerase with L-ribose
ComponentsL-ribose isomerase
KeywordsISOMERASE / cupin-type beta-barrel
Function / homology
Function and homology information


isomerase activity / metal ion binding
Similarity search - Function
RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-L-ribopyranose / : / L-ribose / L-ribose isomerase
Similarity search - Component
Biological speciesCellulomonas parahominis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTerami, Y. / Yoshida, H. / Takata, G. / Kamitori, S.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Essentiality of tetramer formation of Cellulomonas parahominis L-ribose isomerase involved in novel L-ribose metabolic pathway.
Authors: Terami, Y. / Yoshida, H. / Uechi, K. / Morimoto, K. / Takata, G. / Kamitori, S.
History
DepositionJun 13, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 1, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_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.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_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Aug 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-ribose isomerase
B: L-ribose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3968
Polymers56,6852
Non-polymers7106
Water3,783210
1
A: L-ribose isomerase
B: L-ribose isomerase
hetero molecules

A: L-ribose isomerase
B: L-ribose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,79216
Polymers113,3714
Non-polymers1,42112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area13040 Å2
ΔGint-67 kcal/mol
Surface area34360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.730, 88.550, 152.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein L-ribose isomerase


Mass: 28342.680 Da / Num. of mol.: 2 / Mutation: F121L, L125F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas parahominis (bacteria) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: L0N3Y0
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Sugar ChemComp-0MK / beta-L-ribopyranose / beta-L-ribose / L-ribose / ribose / L-ribopyranose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 3
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-ROR / L-ribose


Type: L-saccharide / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 3.9M ammonium acetate, 0.1M sodium acetate trihydrate, pH 4.6, 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: Nov 8, 2013
RadiationMonochromator: CONFOCAL Eliptical Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→19.33 Å / Num. all: 38090 / Num. obs: 37576 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.4
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3791 / % possible all: 96.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.3refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.33 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 5344503.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3758 10 %RANDOM
Rwork0.202 ---
all0.206 38090 --
obs0.206 37539 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.7204 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.4 Å20 Å20 Å2
2--1.31 Å20 Å2
3---2.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 42 210 4016
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_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 1.95→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.361 387 10.6 %
Rwork0.326 3278 -
obs--96.7 %
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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