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- PDB-3a9s: X-ray Structure of Bacillus pallidus D-Arabinose Isomerase Comple... -

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Basic information

Entry
Database: PDB / ID: 3a9s
TitleX-ray Structure of Bacillus pallidus D-Arabinose Isomerase Complex with Glycerol
ComponentsD-arabinose isomerase
KeywordsISOMERASE / Rossmann fold / beta barrel / Carbohydrate metabolism / Cytoplasm / Fucose metabolism / Manganese / Metal-binding
Function / homology
Function and homology information


arabinose isomerase activity / L-fucose isomerase / L-fucose isomerase activity / D-arabinose catabolic process / L-fucose catabolic process / manganese ion binding / cytoplasm
Similarity search - Function
L-fucose Isomerase; Chain A, domain 3 / L-fucose/L-arabinose isomerase, C-terminal / L-fucose Isomerase; Chain A, domain 2 / L-fucose Isomerase; Chain A, domain 2 / Rossmann fold - #1070 / L-fucose isomerase / L-fucose isomerase, N-terminal-1 / L-fucose isomerase, N-terminal-2 / L-fucose isomerase, C-terminal / L-fucose isomerase, domain 1 superfamily ...L-fucose Isomerase; Chain A, domain 3 / L-fucose/L-arabinose isomerase, C-terminal / L-fucose Isomerase; Chain A, domain 2 / L-fucose Isomerase; Chain A, domain 2 / Rossmann fold - #1070 / L-fucose isomerase / L-fucose isomerase, N-terminal-1 / L-fucose isomerase, N-terminal-2 / L-fucose isomerase, C-terminal / L-fucose isomerase, domain 1 superfamily / L-fucose isomerase, domain 2 superfamily / L-fucose isomerase, domain 3 superfamily / L-fucose isomerase, C-terminal domain / L-fucose isomerase, first N-terminal domain / L-fucose isomerase, second N-terminal domain / L-fucose/L-arabinose isomerase, C-terminal / L-fucose isomerase, N-terminal/central domain superfamily / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / L-fucose isomerase
Similarity search - Component
Biological speciesGeobacillus pallidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTakeda, K. / Yoshida, H. / Izumori, K. / Kamitori, S.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: X-ray structures of Bacillus pallidusd-arabinose isomerase and its complex with l-fucitol.
Authors: Takeda, K. / Yoshida, H. / Izumori, K. / Kamitori, S.
History
DepositionNov 5, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: 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_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_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-arabinose isomerase
B: D-arabinose isomerase
C: D-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,54215
Polymers198,6603
Non-polymers88212
Water28,4461579
1
A: D-arabinose isomerase
B: D-arabinose isomerase
C: D-arabinose isomerase
hetero molecules

A: D-arabinose isomerase
B: D-arabinose isomerase
C: D-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)399,08530
Polymers397,3206
Non-polymers1,76424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area42250 Å2
ΔGint-90 kcal/mol
Surface area97470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.317, 127.271, 110.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein D-arabinose isomerase


Mass: 66220.047 Da / Num. of mol.: 3 / Mutation: E225G, N589K, F590L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus pallidus (bacteria) / Strain: 14a / Gene: dai / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: C0SSE7, D-arabinose isomerase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1579 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM citrate buffer pH 6.0, 20% (w/v) PEG 3000, 90mM potassium sodium tartrate. , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 9, 2008
RadiationMonochromator: Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 267379 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 17.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 4.3 / Num. unique all: 24632 / % possible all: 92.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FUI

1fui


Resolution: 1.6→40.7 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 125897.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.187 24951 10 %RANDOM
Rwork0.168 ---
all0.17 ---
obs0.168 248934 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.1529 Å2 / ksol: 0.380111 e/Å3
Displacement parametersBiso mean: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2---1.17 Å20 Å2
3---2.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13818 0 48 1579 15445
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.231 2243 10.1 %
Rwork0.213 19968 -
obs--84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5glycerol.parampsicose.top

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