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- PDB-1de5: L-RHAMNOSE ISOMERASE -

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Basic information

Entry
Database: PDB / ID: 1de5
TitleL-RHAMNOSE ISOMERASE
ComponentsL-RHAMNOSE ISOMERASE
KeywordsISOMERASE / (BETA8/ALPHA8) BARREL / TIM BARREL / HYDRIDE SHIFT
Function / homology
Function and homology information


L-rhamnose isomerase / L-rhamnose isomerase activity / rhamnose binding / L-lyxose metabolic process / rhamnose catabolic process / manganese ion binding / protein homotetramerization / protein-containing complex / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Rhamnose isomerase / L-rhamnose isomerase (RhaA) / : / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
L-RHAMNITOL / L-rhamnose isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsKorndorfer, I.P. / Fessner, W.D. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution.
Authors: Korndorfer, I.P. / Fessner, W.D. / Matthews, B.W.
History
DepositionNov 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-RHAMNOSE ISOMERASE
B: L-RHAMNOSE ISOMERASE
C: L-RHAMNOSE ISOMERASE
D: L-RHAMNOSE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,60812
Polymers192,6814
Non-polymers9268
Water18,4471024
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21860 Å2
ΔGint-206 kcal/mol
Surface area50270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.442, 162.693, 77.022
Angle α, β, γ (deg.)90.00, 110.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
L-RHAMNOSE ISOMERASE


Mass: 48170.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET28B(+) / Production host: Escherichia coli (E. coli) / Variant (production host): PIK61 / References: UniProt: P32170, L-rhamnose isomerase
#2: Sugar
ChemComp-RNT / L-RHAMNITOL


Type: L-saccharide / Mass: 166.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O5
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1024 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.2 M CITRATE, 0.1-M HEPES, 22.5 - 30.0 % PEG 8000, 10 % ISOPROPANOL, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMHEPES1drop
3100 mM1dropNaCl
40.2 Mcitrate1reservoir
50.1 MHEPES1reservoir
622.5-30.0 %(w/w)PEG80001reservoir
710 %(w/w)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 195 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 156599 / Num. obs: 85683 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / % possible all: 88
Reflection shell
*PLUS
% possible obs: 88 %

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
TNTphasing
RefinementResolution: 2.2→15 Å / Stereochemistry target values: TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.275 4376 -SAME AS REFERENCE STRUCTURE 1DW8
Rwork0.156 ---
all0.162 85683 --
obs0.156 81307 81 %-
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13243 0 48 1024 14315
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.6
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.3
X-RAY DIFFRACTIONt_plane_restr0.014

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